4QXX
HEADER PROTEIN FIBRIL 22-JUL-14 4QXX TITLE STRUCTURE OF THE AMYLOID FORMING PEPTIDE GNLVS (RESIDUES 26-30) FROM TITLE 2 THE EOSINOPHIL MAJOR BASIC PROTEIN (EMBP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BONE MARROW PROTEOGLYCAN; COMPND 3 CHAIN: Z; COMPND 4 FRAGMENT: GNLVS PEPTIDE (UNP RESIDUES 131-135); COMPND 5 SYNONYM: BMPG, PROTEOGLYCAN 2, EOSINOPHIL GRANULE MAJOR BASIC COMPND 6 PROTEIN, EMBP, MBP, PREGNANCY-ASSOCIATED MAJOR BASIC PROTEIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS AMYLOID-LIKE PROTOFIBRIL, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR A.B.SORIAGA,A.SORAGNI,M.R.SAWAYA,D.EISENBERG REVDAT 3 28-FEB-24 4QXX 1 REMARK REVDAT 2 08-APR-15 4QXX 1 JRNL REVDAT 1 18-MAR-15 4QXX 0 JRNL AUTH A.SORAGNI,S.YOUSEFI,C.STOECKLE,A.B.SORIAGA,M.R.SAWAYA, JRNL AUTH 2 E.KOZLOWSKI,I.SCHMID,S.RADONJIC-HOESLI,S.BOUTET, JRNL AUTH 3 G.J.WILLIAMS,M.MESSERSCHMIDT,M.M.SEIBERT,D.CASCIO, JRNL AUTH 4 N.A.ZATSEPIN,M.BURGHAMMER,C.RIEKEL,J.P.COLLETIER,R.RIEK, JRNL AUTH 5 D.S.EISENBERG,H.U.SIMON JRNL TITL TOXICITY OF EOSINOPHIL MBP IS REPRESSED BY INTRACELLULAR JRNL TITL 2 CRYSTALLIZATION AND PROMOTED BY EXTRACELLULAR AGGREGATION. JRNL REF MOL.CELL V. 57 1011 2015 JRNL REFN ISSN 1097-2765 JRNL PMID 25728769 JRNL DOI 10.1016/J.MOLCEL.2015.01.026 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 64 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 17.8809 - 1.4450 0.98 574 64 0.1641 0.1918 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 49.59 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06950 REMARK 3 B22 (A**2) : -0.22460 REMARK 3 B33 (A**2) : 0.29400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 33 REMARK 3 ANGLE : 1.269 44 REMARK 3 CHIRALITY : 0.069 6 REMARK 3 PLANARITY : 0.002 6 REMARK 3 DIHEDRAL : 9.426 11 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4QXX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086652. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(220) SIDE BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 658 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.445 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.46000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3600 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 15.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 0.1 M REMARK 280 PHOSPHATE/CITRATE, PH 4.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 8.40800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 17.87950 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 8.40800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.87950 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 300 REMARK: THE BIOLOGICAL ASSEMBLY LISTED IN REMARK 350 REPRESENTS REMARK 300 ONLY A SEGMENT OF A FIBRIL. 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: Z 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 4.75500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 9.51000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 8.40800 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 17.87950 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 4.75500 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 8.40800 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 17.87950 REMARK 350 BIOMT1 6 -1.000000 0.000000 0.000000 9.51000 REMARK 350 BIOMT2 6 0.000000 1.000000 0.000000 8.40800 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 17.87950 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH Z 102 LIES ON A SPECIAL POSITION. DBREF 4QXX Z 1 5 UNP P13727 PRG2_HUMAN 131 135 SEQRES 1 Z 5 GLY ASN LEU VAL SER FORMUL 2 HOH *2(H2 O) CRYST1 4.755 16.816 35.759 90.00 90.00 90.00 P 2 21 21 4 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 0.210305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.059467 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027965 0.00000 ATOM 1 N GLY Z 1 -0.821 -2.072 16.609 1.00 9.93 N ANISOU 1 N GLY Z 1 1184 1952 638 314 -191 -326 N ATOM 2 CA GLY Z 1 -1.705 -2.345 15.487 1.00 7.38 C ANISOU 2 CA GLY Z 1 957 1374 472 279 -124 -261 C ATOM 3 C GLY Z 1 -0.968 -3.008 14.344 1.00 4.89 C ANISOU 3 C GLY Z 1 899 614 343 211 112 -106 C ATOM 4 O GLY Z 1 0.258 -2.982 14.292 1.00 5.05 O ANISOU 4 O GLY Z 1 839 595 485 -11 -7 -180 O ATOM 5 N ASN Z 2 -1.721 -3.603 13.425 1.00 3.53 N ANISOU 5 N ASN Z 2 747 329 264 -226 117 -67 N ATOM 6 CA ASN Z 2 -1.141 -4.323 12.291 1.00 1.85 C ANISOU 6 CA ASN Z 2 313 164 225 76 -23 77 C ATOM 7 C ASN Z 2 -1.748 -3.900 10.968 1.00 3.00 C ANISOU 7 C ASN Z 2 610 293 238 197 -2 -42 C ATOM 8 O ASN Z 2 -2.955 -3.683 10.873 1.00 3.99 O ANISOU 8 O ASN Z 2 599 514 402 199 191 -60 O ATOM 9 CB ASN Z 2 -1.353 -5.827 12.446 1.00 5.03 C ANISOU 9 CB ASN Z 2 1173 368 369 170 -47 37 C ATOM 10 CG ASN Z 2 -0.679 -6.391 13.683 1.00 5.08 C ANISOU 10 CG ASN Z 2 727 718 484 228 -243 90 C ATOM 11 OD1 ASN Z 2 0.519 -6.202 13.896 1.00 6.10 O ANISOU 11 OD1 ASN Z 2 828 960 531 477 -61 100 O ATOM 12 ND2 ASN Z 2 -1.448 -7.087 14.506 1.00 8.41 N ANISOU 12 ND2 ASN Z 2 1513 1193 488 40 102 279 N ATOM 13 N LEU Z 3 -0.907 -3.803 9.944 1.00 3.47 N ANISOU 13 N LEU Z 3 701 405 213 -242 25 -26 N ATOM 14 CA LEU Z 3 -1.388 -3.576 8.586 1.00 3.48 C ANISOU 14 CA LEU Z 3 728 324 271 79 180 -5 C ATOM 15 C LEU Z 3 -0.783 -4.660 7.709 1.00 3.29 C ANISOU 15 C LEU Z 3 684 261 306 -17 150 -80 C ATOM 16 O LEU Z 3 0.437 -4.788 7.643 1.00 3.80 O ANISOU 16 O LEU Z 3 590 437 415 141 178 -122 O ATOM 17 CB LEU Z 3 -0.977 -2.185 8.081 1.00 3.88 C ANISOU 17 CB LEU Z 3 899 293 282 171 125 42 C ATOM 18 CG LEU Z 3 -1.524 -1.669 6.736 1.00 8.66 C ANISOU 18 CG LEU Z 3 2091 598 600 63 -94 66 C ATOM 19 CD1 LEU Z 3 -1.225 -0.191 6.570 1.00 9.89 C ANISOU 19 CD1 LEU Z 3 2263 792 703 132 -163 143 C ATOM 20 CD2 LEU Z 3 -0.962 -2.409 5.541 1.00 13.56 C ANISOU 20 CD2 LEU Z 3 3203 1048 901 -640 -305 94 C ATOM 21 N VAL Z 4 -1.635 -5.424 7.029 1.00 3.17 N ANISOU 21 N VAL Z 4 604 266 333 -100 104 -123 N ATOM 22 CA VAL Z 4 -1.165 -6.460 6.119 1.00 3.61 C ANISOU 22 CA VAL Z 4 607 353 411 205 -241 -157 C ATOM 23 C VAL Z 4 -1.791 -6.230 4.755 1.00 5.31 C ANISOU 23 C VAL Z 4 543 915 562 395 -15 -39 C ATOM 24 O VAL Z 4 -3.014 -6.209 4.620 1.00 7.31 O ANISOU 24 O VAL Z 4 577 1569 630 45 -5 -227 O ATOM 25 CB VAL Z 4 -1.567 -7.872 6.593 1.00 5.31 C ANISOU 25 CB VAL Z 4 1024 336 657 64 39 -167 C ATOM 26 CG1 VAL Z 4 -1.012 -8.934 5.633 1.00 6.73 C ANISOU 26 CG1 VAL Z 4 1131 549 879 220 104 -300 C ATOM 27 CG2 VAL Z 4 -1.083 -8.120 8.018 1.00 5.48 C ANISOU 27 CG2 VAL Z 4 819 632 630 15 15 42 C ATOM 28 N SER Z 5 -0.966 -6.052 3.736 1.00 7.53 N ANISOU 28 N SER Z 5 810 1357 693 337 48 302 N ATOM 29 CA SER Z 5 -1.526 -5.888 2.407 1.00 11.48 C ANISOU 29 CA SER Z 5 1654 1766 943 560 -145 241 C ATOM 30 C SER Z 5 -1.207 -7.085 1.529 1.00 16.35 C ANISOU 30 C SER Z 5 3066 2118 1029 758 -523 -208 C ATOM 31 O SER Z 5 -0.437 -7.976 1.902 1.00 14.00 O ANISOU 31 O SER Z 5 2584 1676 1060 878 -402 -452 O ATOM 32 CB SER Z 5 -1.031 -4.596 1.767 1.00 13.36 C ANISOU 32 CB SER Z 5 1565 2151 1361 818 -30 608 C ATOM 33 OG SER Z 5 0.361 -4.652 1.540 1.00 15.80 O ANISOU 33 OG SER Z 5 1604 2812 1587 822 25 763 O ATOM 34 OXT SER Z 5 -1.737 -7.178 0.429 1.00 17.09 O ANISOU 34 OXT SER Z 5 2807 2495 1192 648 -712 -430 O TER 35 SER Z 5 HETATM 36 O HOH Z 101 0.935 -5.175 16.502 1.00 18.83 O ANISOU 36 O HOH Z 101 3066 2772 1315 -1227 -232 339 O HETATM 37 O AHOH Z 102 0.691 -8.408 17.879 0.91 56.55 O ANISOU 37 O AHOH Z 102 9673 9234 2579 0 5 1219 O HETATM 38 O BHOH Z 102 -0.788 -9.006 16.641 0.09 38.95 O ANISOU 38 O BHOH Z 102 6801 4266 3734 2095 -1531 549 O MASTER 214 0 0 0 0 0 0 6 36 1 0 1 END
