1O06
HEADER TRANSPORT PROTEIN 20-FEB-03 1O06 TITLE CRYSTAL STRUCTURE OF THE VPS27P UBIQUITIN INTERACTING MOTIF (UIM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS27; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 301-320; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN SACCHAROMYCES SOURCE 4 CEREVISIAE VPS27P AND WAS SYNTHESIZED BY STANDARD PEPTIDE SYNTHESIS SOURCE 5 METHODS KEYWDS ALPHA-HELIX, COILED-COIL, TETRAMER, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.D.FISHER,B.WANG,S.L.ALAM,D.S.HIGGINSON,R.RICH,D.MYSZKA, AUTHOR 2 W.I.SUNDQUIST,C.P.HILL REVDAT 5 14-FEB-24 1O06 1 REMARK LINK REVDAT 4 13-JUL-11 1O06 1 VERSN REVDAT 3 24-FEB-09 1O06 1 VERSN REVDAT 2 01-MAR-05 1O06 1 REVDAT 1 22-JUL-03 1O06 0 JRNL AUTH R.D.FISHER,B.WANG,S.L.ALAM,D.S.HIGGINSON,H.ROBINSON, JRNL AUTH 2 W.I.SUNDQUIST,C.P.HILL JRNL TITL STRUCTURE AND UBIQUITIN BINDING OF THE UBIQUITIN-INTERACTING JRNL TITL 2 MOTIF. JRNL REF J.BIOL.CHEM. V. 278 28976 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12750381 JRNL DOI 10.1074/JBC.M302596200 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 4053 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 443 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 262 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.2590 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 157 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -0.67000 REMARK 3 B12 (A**2) : 0.22000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.070 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.026 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 174 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 146 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 236 ; 1.365 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): 350 ; 0.733 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 23 ; 3.116 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 25 ; 0.051 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 211 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 26 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 49 ; 0.346 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 177 ; 0.254 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 102 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 20 ; 0.293 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.205 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.341 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 13 ; 0.142 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.280 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 113 ; 0.681 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 180 ; 1.340 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 61 ; 2.418 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 56 ; 4.260 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1O06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JAN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4525 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M SODIUM CACODYLATE, 0.16M ZINC REMARK 280 ACETATE, 10.4% PEG-8000, 20% GLYCEROL, PH 6.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.82867 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.41433 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.82867 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.41433 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.82867 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 21.41433 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 42.82867 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 21.41433 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 60.56462 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 17.48350 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 90.84693 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 1 N REMARK 620 2 GLU A 18 OE1 84.6 REMARK 620 3 ALA A 20 OXT 84.7 110.7 REMARK 620 4 ALA A 20 O 143.8 122.2 64.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 1 N REMARK 620 2 GLU A 18 OE1 115.2 REMARK 620 3 ALA A 20 OXT 96.5 106.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 3 OD2 REMARK 620 2 ASP A 5 OD2 129.2 REMARK 620 3 ASP A 5 OD1 91.0 51.1 REMARK 620 4 GLU A 16 OE1 96.4 109.2 157.3 REMARK 620 5 GLU A 19 OE1 96.8 116.0 94.5 105.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 5 OD2 REMARK 620 2 ASP A 5 OD2 82.3 REMARK 620 3 GLU A 16 OE2 91.4 113.9 REMARK 620 4 GLU A 16 OE2 116.5 81.1 150.5 REMARK 620 5 HOH A 205 O 85.6 148.2 95.7 78.3 REMARK 620 6 HOH A 205 O 146.8 75.1 76.2 84.0 125.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 103 DBREF 1O06 A 1 20 UNP P40343 VPS27_YEAST 301 320 SEQRES 1 A 20 GLU GLU ASP PRO ASP LEU LYS ALA ALA ILE GLN GLU SER SEQRES 2 A 20 LEU ARG GLU ALA GLU GLU ALA HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 2 HETNAM ZN ZINC ION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 HOH *26(H2 O) HELIX 1 1 ASP A 3 GLU A 19 1 17 LINK N GLU A 1 ZN B ZN A 103 1555 1555 2.54 LINK N GLU A 1 ZN A ZN A 103 1555 1555 1.79 LINK OD2 ASP A 3 ZN ZN A 101 12575 1555 1.91 LINK OD2 ASP A 5 ZN ZN A 101 1555 1555 1.92 LINK OD1 ASP A 5 ZN ZN A 101 1555 1555 2.73 LINK OD2 ASP A 5 ZN ZN A 102 1555 1555 2.31 LINK OD2 ASP A 5 ZN ZN A 102 12575 1555 2.56 LINK OE1 GLU A 16 ZN ZN A 101 9665 1555 1.96 LINK OE2 GLU A 16 ZN ZN A 102 9665 1555 2.11 LINK OE2 GLU A 16 ZN ZN A 102 4675 1555 2.30 LINK OE1 GLU A 18 ZN B ZN A 103 11665 1555 2.36 LINK OE1 GLU A 18 ZN A ZN A 103 11665 1555 2.11 LINK OE1 GLU A 19 ZN ZN A 101 9665 1555 2.01 LINK OXT ALA A 20 ZN B ZN A 103 8675 1555 1.77 LINK O ALA A 20 ZN B ZN A 103 8675 1555 2.09 LINK OXT ALA A 20 ZN A ZN A 103 8675 1555 2.16 LINK ZN ZN A 102 O HOH A 205 1555 4675 2.24 LINK ZN ZN A 102 O HOH A 205 1555 9665 2.51 SITE 1 AC1 5 ASP A 3 ASP A 5 GLU A 16 GLU A 19 SITE 2 AC1 5 ZN A 102 SITE 1 AC2 4 ASP A 5 GLU A 16 ZN A 101 HOH A 205 SITE 1 AC3 3 GLU A 1 GLU A 18 ALA A 20 CRYST1 34.967 34.967 64.243 90.00 90.00 120.00 P 62 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.028598 0.016511 0.000000 0.00000 SCALE2 0.000000 0.033023 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015566 0.00000 ATOM 1 N GLU A 1 5.336 48.768 2.165 1.00 20.67 N ATOM 2 CA GLU A 1 5.263 48.062 3.466 1.00 21.08 C ATOM 3 C GLU A 1 4.813 46.626 3.230 1.00 19.87 C ATOM 4 O GLU A 1 3.705 46.391 2.744 1.00 20.55 O ATOM 5 CB GLU A 1 4.285 48.768 4.404 1.00 21.76 C ATOM 6 CG GLU A 1 4.313 48.261 5.837 1.00 24.53 C ATOM 7 CD GLU A 1 5.484 48.788 6.643 1.00 27.66 C ATOM 8 OE1 GLU A 1 5.616 48.368 7.812 1.00 30.19 O ATOM 9 OE2 GLU A 1 6.273 49.617 6.128 1.00 29.83 O ATOM 10 N GLU A 2 5.682 45.678 3.554 1.00 18.60 N ATOM 11 CA GLU A 2 5.335 44.267 3.533 1.00 17.49 C ATOM 12 C GLU A 2 4.713 43.867 4.863 1.00 16.56 C ATOM 13 O GLU A 2 4.893 44.528 5.883 1.00 17.43 O ATOM 14 CB GLU A 2 6.566 43.426 3.217 1.00 17.43 C ATOM 15 CG GLU A 2 7.156 43.722 1.840 1.00 17.86 C ATOM 16 CD GLU A 2 8.554 43.178 1.654 1.00 19.42 C ATOM 17 OE1 GLU A 2 8.932 42.208 2.334 1.00 22.63 O ATOM 18 OE2 GLU A 2 9.288 43.733 0.807 1.00 18.92 O ATOM 19 N ASP A 3 3.954 42.787 4.826 1.00 14.95 N ATOM 20 CA ASP A 3 3.197 42.328 5.975 1.00 13.54 C ATOM 21 C ASP A 3 3.865 41.054 6.472 1.00 12.30 C ATOM 22 O ASP A 3 3.845 40.037 5.779 1.00 11.46 O ATOM 23 CB ASP A 3 1.758 42.081 5.529 1.00 13.36 C ATOM 24 CG ASP A 3 0.838 41.721 6.662 1.00 12.91 C ATOM 25 OD1 ASP A 3 1.275 41.047 7.616 1.00 12.69 O ATOM 26 OD2 ASP A 3 -0.357 42.073 6.661 1.00 12.66 O ATOM 27 N PRO A 4 4.474 41.075 7.652 1.00 11.87 N ATOM 28 CA PRO A 4 5.178 39.874 8.121 1.00 10.76 C ATOM 29 C PRO A 4 4.260 38.675 8.341 1.00 10.51 C ATOM 30 O PRO A 4 4.720 37.551 8.216 1.00 9.80 O ATOM 31 CB PRO A 4 5.838 40.318 9.436 1.00 11.76 C ATOM 32 CG PRO A 4 5.129 41.527 9.844 1.00 13.13 C ATOM 33 CD PRO A 4 4.564 42.176 8.624 1.00 11.71 C ATOM 34 N ASP A 5 2.990 38.892 8.657 1.00 9.07 N ATOM 35 CA ASP A 5 2.077 37.780 8.856 1.00 9.21 C ATOM 36 C ASP A 5 1.731 37.113 7.534 1.00 8.99 C ATOM 37 O ASP A 5 1.530 35.914 7.498 1.00 9.57 O ATOM 38 CB ASP A 5 0.776 38.233 9.501 1.00 9.20 C ATOM 39 CG ASP A 5 0.868 38.388 11.001 1.00 10.42 C ATOM 40 OD1 ASP A 5 1.892 38.092 11.648 1.00 12.19 O ATOM 41 OD2 ASP A 5 -0.127 38.788 11.634 1.00 10.42 O ATOM 42 N LEU A 6 1.623 37.894 6.465 1.00 9.06 N ATOM 43 CA LEU A 6 1.399 37.327 5.136 1.00 9.52 C ATOM 44 C LEU A 6 2.573 36.444 4.752 1.00 9.92 C ATOM 45 O LEU A 6 2.379 35.314 4.344 1.00 9.30 O ATOM 46 CB LEU A 6 1.187 38.436 4.086 1.00 10.01 C ATOM 47 CG LEU A 6 1.039 37.955 2.634 1.00 10.89 C ATOM 48 CD1 LEU A 6 -0.117 36.970 2.447 1.00 12.60 C ATOM 49 CD2 LEU A 6 0.885 39.149 1.730 1.00 13.00 C ATOM 50 N LYS A 7 3.787 36.957 4.894 1.00 9.30 N ATOM 51 CA LYS A 7 4.976 36.211 4.521 1.00 10.12 C ATOM 52 C LYS A 7 5.111 34.969 5.394 1.00 9.96 C ATOM 53 O LYS A 7 5.434 33.893 4.890 1.00 9.24 O ATOM 54 CB LYS A 7 6.207 37.103 4.610 1.00 10.93 C ATOM 55 CG LYS A 7 6.160 38.212 3.572 0.50 11.22 C ATOM 56 CD LYS A 7 7.466 38.955 3.475 1.00 14.78 C ATOM 57 CE LYS A 7 7.706 39.855 4.672 0.50 14.94 C ATOM 58 NZ LYS A 7 8.973 40.616 4.509 0.50 15.74 N ATOM 59 N ALA A 8 4.830 35.081 6.684 1.00 10.11 N ATOM 60 CA ALA A 8 4.978 33.947 7.584 1.00 10.14 C ATOM 61 C ALA A 8 3.991 32.840 7.222 1.00 9.97 C ATOM 62 O ALA A 8 4.335 31.657 7.266 1.00 10.37 O ATOM 63 CB ALA A 8 4.794 34.376 9.035 1.00 10.75 C ATOM 64 N ALA A 9 2.769 33.210 6.848 1.00 10.06 N ATOM 65 CA ALA A 9 1.751 32.241 6.487 1.00 9.79 C ATOM 66 C ALA A 9 2.139 31.512 5.205 1.00 9.72 C ATOM 67 O ALA A 9 1.966 30.304 5.082 1.00 9.20 O ATOM 68 CB ALA A 9 0.391 32.912 6.339 1.00 9.94 C ATOM 69 N ILE A 10 2.701 32.240 4.251 1.00 8.99 N ATOM 70 CA ILE A 10 3.131 31.619 3.003 1.00 9.39 C ATOM 71 C ILE A 10 4.347 30.714 3.231 1.00 9.83 C ATOM 72 O ILE A 10 4.421 29.623 2.673 1.00 9.70 O ATOM 73 CB ILE A 10 3.434 32.704 1.946 1.00 9.40 C ATOM 74 CG1 ILE A 10 2.175 33.486 1.577 1.00 9.56 C ATOM 75 CG2 ILE A 10 4.033 32.074 0.679 1.00 10.01 C ATOM 76 CD1 ILE A 10 2.465 34.770 0.856 1.00 10.26 C ATOM 77 N AGLN A 11 5.310 31.181 4.025 0.50 10.18 N ATOM 78 N BGLN A 11 5.301 31.160 4.041 0.50 10.09 N ATOM 79 CA AGLN A 11 6.476 30.372 4.362 0.50 10.84 C ATOM 80 CA BGLN A 11 6.470 30.341 4.333 0.50 10.66 C ATOM 81 C AGLN A 11 6.035 29.070 5.020 0.50 10.57 C ATOM 82 C BGLN A 11 6.057 29.061 5.046 0.50 10.52 C ATOM 83 O AGLN A 11 6.558 27.995 4.701 0.50 10.46 O ATOM 84 O BGLN A 11 6.623 27.989 4.793 0.50 10.47 O ATOM 85 CB AGLN A 11 7.438 31.133 5.283 0.50 11.27 C ATOM 86 CB BGLN A 11 7.491 31.120 5.159 0.50 10.92 C ATOM 87 CG AGLN A 11 8.317 32.154 4.567 0.50 13.23 C ATOM 88 CG BGLN A 11 8.114 32.275 4.397 0.50 12.49 C ATOM 89 CD AGLN A 11 8.820 33.265 5.488 0.50 15.18 C ATOM 90 CD BGLN A 11 9.355 31.882 3.619 0.50 14.32 C ATOM 91 OE1AGLN A 11 8.840 33.108 6.704 0.50 17.98 O ATOM 92 OE1BGLN A 11 9.605 30.697 3.374 0.50 15.67 O ATOM 93 NE2AGLN A 11 9.202 34.397 4.901 0.50 17.75 N ATOM 94 NE2BGLN A 11 10.142 32.879 3.231 0.50 15.74 N ATOM 95 N GLU A 12 5.073 29.162 5.935 1.00 10.67 N ATOM 96 CA GLU A 12 4.538 27.984 6.592 1.00 10.67 C ATOM 97 C GLU A 12 3.898 27.049 5.566 1.00 10.19 C ATOM 98 O GLU A 12 4.118 25.836 5.637 1.00 9.81 O ATOM 99 CB GLU A 12 3.526 28.354 7.686 1.00 11.31 C ATOM 100 CG GLU A 12 3.038 27.169 8.508 1.00 15.91 C ATOM 101 CD GLU A 12 4.168 26.437 9.217 1.00 20.56 C ATOM 102 OE1 GLU A 12 5.209 27.059 9.536 1.00 25.79 O ATOM 103 OE2 GLU A 12 4.039 25.223 9.463 1.00 26.21 O ATOM 104 N ASER A 13 3.130 27.624 4.641 0.50 9.47 N ATOM 105 N BSER A 13 3.119 27.554 4.600 0.50 9.80 N ATOM 106 CA ASER A 13 2.518 26.866 3.557 0.50 9.62 C ATOM 107 CA BSER A 13 2.563 26.619 3.599 0.50 9.89 C ATOM 108 C ASER A 13 3.562 26.061 2.778 0.50 9.92 C ATOM 109 C BSER A 13 3.645 25.952 2.805 0.50 10.20 C ATOM 110 O ASER A 13 3.309 24.911 2.432 0.50 9.46 O ATOM 111 O BSER A 13 3.497 24.799 2.428 0.50 9.69 O ATOM 112 CB ASER A 13 1.739 27.798 2.615 0.50 9.70 C ATOM 113 CB BSER A 13 1.584 27.220 2.589 0.50 10.61 C ATOM 114 OG ASER A 13 0.682 28.457 3.293 0.70 10.95 O ATOM 115 OG BSER A 13 2.067 28.396 1.972 0.30 9.81 O ATOM 116 N LEU A 14 4.720 26.671 2.507 1.00 10.29 N ATOM 117 CA LEU A 14 5.814 26.041 1.770 1.00 11.60 C ATOM 118 C LEU A 14 6.411 24.874 2.544 1.00 11.84 C ATOM 119 O LEU A 14 6.633 23.814 1.965 1.00 12.48 O ATOM 120 CB LEU A 14 6.882 27.067 1.393 1.00 12.53 C ATOM 121 CG LEU A 14 7.904 26.580 0.366 1.00 15.29 C ATOM 122 CD1 LEU A 14 7.269 26.379 -1.000 1.00 17.32 C ATOM 123 CD2 LEU A 14 9.042 27.573 0.275 1.00 17.44 C ATOM 124 N ARG A 15 6.627 25.048 3.841 1.00 12.02 N ATOM 125 CA ARG A 15 7.159 23.986 4.681 1.00 12.70 C ATOM 126 C ARG A 15 6.172 22.834 4.710 1.00 12.01 C ATOM 127 O ARG A 15 6.551 21.669 4.622 1.00 12.87 O ATOM 128 CB ARG A 15 7.412 24.485 6.097 1.00 13.79 C ATOM 129 CG ARG A 15 8.687 25.229 6.260 1.00 17.83 C ATOM 130 CD ARG A 15 9.053 25.443 7.710 1.00 22.20 C ATOM 131 NE ARG A 15 8.315 26.579 8.244 1.00 24.85 N ATOM 132 CZ ARG A 15 8.621 27.857 8.014 1.00 26.83 C ATOM 133 NH1 ARG A 15 9.674 28.194 7.270 1.00 27.76 N ATOM 134 NH2 ARG A 15 7.867 28.804 8.538 1.00 27.23 N ATOM 135 N GLU A 16 4.894 23.170 4.819 1.00 11.44 N ATOM 136 CA GLU A 16 3.834 22.171 4.828 1.00 11.37 C ATOM 137 C GLU A 16 3.765 21.364 3.526 1.00 11.84 C ATOM 138 O GLU A 16 3.578 20.141 3.547 1.00 12.73 O ATOM 139 CB GLU A 16 2.488 22.847 5.108 1.00 11.22 C ATOM 140 CG GLU A 16 2.315 23.267 6.551 1.00 10.93 C ATOM 141 CD GLU A 16 2.152 22.092 7.476 1.00 11.05 C ATOM 142 OE1 GLU A 16 1.572 21.079 7.043 1.00 10.12 O ATOM 143 OE2 GLU A 16 2.602 22.213 8.624 1.00 12.92 O ATOM 144 N ALA A 17 3.951 22.032 2.394 1.00 11.94 N ATOM 145 CA ALA A 17 3.898 21.368 1.105 1.00 13.05 C ATOM 146 C ALA A 17 5.061 20.404 0.981 1.00 14.12 C ATOM 147 O ALA A 17 4.946 19.362 0.338 1.00 14.08 O ATOM 148 CB ALA A 17 3.947 22.391 -0.009 1.00 12.78 C ATOM 149 N GLU A 18 6.183 20.762 1.596 1.00 15.34 N ATOM 150 CA GLU A 18 7.379 19.925 1.576 1.00 17.45 C ATOM 151 C GLU A 18 7.229 18.652 2.399 1.00 17.87 C ATOM 152 O GLU A 18 8.024 17.730 2.236 1.00 18.98 O ATOM 153 CB GLU A 18 8.588 20.720 2.084 1.00 18.22 C ATOM 154 CG GLU A 18 9.410 21.385 1.003 1.00 21.51 C ATOM 155 CD GLU A 18 10.174 20.396 0.136 1.00 24.41 C ATOM 156 OE1 GLU A 18 10.643 19.339 0.644 1.00 26.38 O ATOM 157 OE2 GLU A 18 10.307 20.687 -1.073 1.00 30.41 O ATOM 158 N GLU A 19 6.241 18.598 3.297 1.00 18.42 N ATOM 159 CA GLU A 19 5.938 17.375 4.062 1.00 18.81 C ATOM 160 C GLU A 19 5.331 16.252 3.265 1.00 20.04 C ATOM 161 O GLU A 19 5.374 15.097 3.699 1.00 20.15 O ATOM 162 CB GLU A 19 4.928 17.654 5.168 1.00 18.76 C ATOM 163 CG GLU A 19 5.476 18.419 6.325 1.00 17.89 C ATOM 164 CD GLU A 19 4.383 18.929 7.237 1.00 15.73 C ATOM 165 OE1 GLU A 19 3.229 18.389 7.207 1.00 12.59 O ATOM 166 OE2 GLU A 19 4.709 19.878 7.972 1.00 17.96 O ATOM 167 N ALA A 20 4.691 16.572 2.146 1.00 20.62 N ATOM 168 CA ALA A 20 4.046 15.549 1.338 1.00 21.72 C ATOM 169 C ALA A 20 5.095 14.621 0.747 1.00 22.11 C ATOM 170 O ALA A 20 6.300 14.799 0.903 1.00 22.95 O ATOM 171 CB ALA A 20 3.206 16.175 0.236 1.00 21.76 C ATOM 172 OXT ALA A 20 4.800 13.629 0.092 1.00 23.39 O TER 173 ALA A 20 HETATM 174 ZN ZN A 101 -0.024 38.570 13.535 1.00 10.90 ZN HETATM 175 ZN ZN A 102 -2.295 38.890 10.840 0.25 8.95 ZN HETATM 176 ZN A ZN A 103 6.330 48.169 0.804 0.50 14.39 ZN HETATM 177 ZN B ZN A 103 6.443 47.482 0.280 0.50 18.45 ZN HETATM 178 O AHOH A 201 7.506 37.269 8.193 0.50 14.30 O HETATM 179 O BHOH A 201 7.442 36.923 8.925 0.50 15.08 O HETATM 180 O HOH A 202 3.450 18.901 -1.994 1.00 19.31 O HETATM 181 O HOH A 203 0.258 30.305 1.384 0.50 11.90 O HETATM 182 O HOH A 204 -1.241 41.876 3.976 1.00 17.91 O HETATM 183 O HOH A 205 2.240 23.914 10.904 1.00 19.77 O HETATM 184 O HOH A 206 6.365 31.000 8.968 1.00 21.47 O HETATM 185 O HOH A 207 7.233 20.338 8.241 1.00 24.04 O HETATM 186 O HOH A 208 9.384 27.897 4.321 1.00 26.16 O HETATM 187 O HOH A 209 8.500 44.896 -0.820 0.50 10.75 O HETATM 188 O HOH A 210 0.267 34.856 9.725 1.00 22.54 O HETATM 189 O HOH A 211 0.817 17.838 -2.085 1.00 25.02 O HETATM 190 O HOH A 212 1.452 45.102 3.228 1.00 27.41 O HETATM 191 O HOH A 213 9.108 39.154 7.784 1.00 45.05 O HETATM 192 O HOH A 214 0.715 45.911 5.513 1.00 36.34 O HETATM 193 O HOH A 215 8.793 20.602 5.781 1.00 19.45 O HETATM 194 O HOH A 216 10.539 25.682 3.265 1.00 40.12 O HETATM 195 O HOH A 217 8.332 45.802 -2.908 0.50 17.07 O HETATM 196 O AHOH A 218 5.602 25.336 11.428 0.50 15.94 O HETATM 197 O BHOH A 218 4.336 24.927 11.485 0.50 9.94 O HETATM 198 O HOH A 219 9.634 48.433 6.904 1.00 22.97 O HETATM 199 O AHOH A 220 8.125 48.232 8.480 0.50 10.09 O HETATM 200 O BHOH A 220 7.744 49.220 8.409 0.50 11.73 O HETATM 201 O HOH A 221 8.028 46.413 11.303 0.50 19.00 O HETATM 202 O HOH A 222 8.041 46.511 5.300 1.00 34.42 O HETATM 203 O HOH A 223 5.252 23.165 8.824 1.00 27.61 O HETATM 204 O HOH A 224 -0.443 29.951 9.399 0.50 30.21 O HETATM 205 O HOH A 225 7.723 23.543 -0.705 1.00 30.11 O HETATM 206 O HOH A 226 10.103 46.124 10.097 0.50 20.02 O CONECT 1 176 177 CONECT 40 174 CONECT 41 174 175 CONECT 174 40 41 CONECT 175 41 CONECT 176 1 CONECT 177 1 MASTER 352 0 3 1 0 0 4 6 186 1 7 2 END
