HEADER HYDROLASE 05-APR-17 5VET TITLE PHOSPHOLIPASE A2, RE-REFINEMENT OF THE PDB STRUCTURE 1JQ8 WITHOUT THE TITLE 2 PUTATIVE COMPLEXED OLIGOPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2 VRV-PL-VIIIA; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DABOIA RUSSELLII PULCHELLA; SOURCE 3 ORGANISM_TAXID: 97228 KEYWDS PHOSPHOLIPASE A2, RE-REFINEMENT, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.WLODAWER,Z.DAUTER,W.MINOR,R.STANFIELD,P.POREBSKI,M.JASKOLSKI, AUTHOR 2 E.POZHARSKI,C.X.WEICHENBERGER,B.RUPP REVDAT 3 20-NOV-24 5VET 1 REMARK REVDAT 2 13-APR-22 5VET 1 AUTHOR JRNL REVDAT 1 20-JUN-18 5VET 0 JRNL AUTH A.WLODAWER,Z.DAUTER,P.J.POREBSKI,W.MINOR,R.STANFIELD, JRNL AUTH 2 M.JASKOLSKI,E.POZHARSKI,C.X.WEICHENBERGER,B.RUPP JRNL TITL DETECT, CORRECT, RETRACT: HOW TO MANAGE INCORRECT STRUCTURAL JRNL TITL 2 MODELS. JRNL REF FEBS J. V. 285 444 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 29113027 JRNL DOI 10.1111/FEBS.14320 REMARK 0 REMARK 0 THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA REMARK 0 IN 1JQ8, DETERMINED BY V.CHANDRA,J.JASTI,P.KAUR,S.DEY,C.BETZEL, REMARK 0 T.P.SINGH REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 1JQ8 REMARK 0 AUTH V.CHANDRA,J.JASTI,P.KAUR,S.DEY,A.SRINIVASAN,C.H.BETZEL, REMARK 0 AUTH 2 T.P.SINGH REMARK 0 TITL DESIGN OF SPECIFIC PEPTIDE INHIBITORS OF PHOSPHOLIPASE A2: REMARK 0 TITL 2 STRUCTURE OF A COMPLEX FORMED BETWEEN RUSSELL'S VIPER REMARK 0 TITL 3 PHOSPHOLIPASE A2 AND A DESIGNED PEPTIDE LEU-ALA-ILE-TYR-SER REMARK 0 TITL 4 (LAIYS). REMARK 0 REF ACTA CRYSTALLOGR. D BIOL. V. 58 1813 2002 REMARK 0 REF 2 CRYSTALLOGR. REMARK 0 REFN ISSN 0907-4449 REMARK 0 PMID 12351825 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 17037 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 861 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1888 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.01000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.846 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227320. REMARK 200 REMARK 200 SEE THE ORIGINAL DATA, ENTRY 1JQ8 REMARK 280 REMARK 280 SEE THE ORIGINAL DATA, ENTRY 1JQ8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 38.79500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.79500 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 1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.18750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.18750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 38.79500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.18750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 38.79500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.41250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.18750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 B 239 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 265 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND1 HIS B 48 O HOH B 201 1.91 REMARK 500 O HOH A 289 O HOH A 296 1.99 REMARK 500 O HOH B 201 O HOH B 266 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 327 O HOH B 327 4566 1.79 REMARK 500 O HOH B 287 O HOH B 287 4566 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 55 50.50 -112.48 REMARK 500 LEU B 55 61.10 -118.88 REMARK 500 LYS B 116 -37.53 -37.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JQ8 RELATED DB: PDB REMARK 900 1JQ8 IS AN ORIGINAL DATA. THE CURRENT ENTRY IS AN ALTERNATIVE REMARK 900 MODELING OF 1JQ8. IN PARTICULAR, THE PUTATIVE OLIGOPEPTIDE LEU-ALA- REMARK 900 ILE-TYR-SER WAS DELETED FROM THE STRUCTURE DBREF 5VET A 1 133 UNP D0VX11 D0VX11_9SAUR 1 121 DBREF 5VET B 1 133 UNP D0VX11 D0VX11_9SAUR 1 121 SEQRES 1 A 121 SER LEU LEU GLU PHE GLY LYS MET ILE LEU GLU GLU THR SEQRES 2 A 121 GLY LYS LEU ALA ILE PRO SER TYR SER SER TYR GLY CYS SEQRES 3 A 121 TYR CYS GLY TRP GLY GLY LYS GLY THR PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 A 121 ASN LEU PRO ASP CYS ASN PRO LYS SER ASP ARG TYR LYS SEQRES 6 A 121 TYR LYS ARG VAL ASN GLY ALA ILE VAL CYS GLU LYS GLY SEQRES 7 A 121 THR SER CYS GLU ASN ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 ALA ALA ILE CYS PHE ARG GLN ASN LEU ASN THR TYR SER SEQRES 9 A 121 LYS LYS TYR MET LEU TYR PRO ASP PHE LEU CYS LYS GLY SEQRES 10 A 121 GLU LEU LYS CYS SEQRES 1 B 121 SER LEU LEU GLU PHE GLY LYS MET ILE LEU GLU GLU THR SEQRES 2 B 121 GLY LYS LEU ALA ILE PRO SER TYR SER SER TYR GLY CYS SEQRES 3 B 121 TYR CYS GLY TRP GLY GLY LYS GLY THR PRO LYS ASP ALA SEQRES 4 B 121 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 B 121 ASN LEU PRO ASP CYS ASN PRO LYS SER ASP ARG TYR LYS SEQRES 6 B 121 TYR LYS ARG VAL ASN GLY ALA ILE VAL CYS GLU LYS GLY SEQRES 7 B 121 THR SER CYS GLU ASN ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 B 121 ALA ALA ILE CYS PHE ARG GLN ASN LEU ASN THR TYR SER SEQRES 9 B 121 LYS LYS TYR MET LEU TYR PRO ASP PHE LEU CYS LYS GLY SEQRES 10 B 121 GLU LEU LYS CYS FORMUL 3 HOH *268(H2 O) HELIX 1 AA1 SER A 1 GLY A 14 1 14 HELIX 2 AA2 LEU A 17 TYR A 22 1 6 HELIX 3 AA3 ASP A 39 ASN A 54 1 16 HELIX 4 AA4 THR A 89 ASN A 109 1 21 HELIX 5 AA5 LEU A 110 TYR A 113 5 4 HELIX 6 AA6 SER A 114 MET A 118 5 5 HELIX 7 AA7 PRO A 121 CYS A 126 5 5 HELIX 8 AA8 LEU B 2 GLY B 14 1 13 HELIX 9 AA9 LEU B 17 TYR B 22 1 6 HELIX 10 AB1 ASP B 39 ASN B 54 1 16 HELIX 11 AB2 THR B 89 ASN B 109 1 21 HELIX 12 AB3 LEU B 110 TYR B 113 5 4 HELIX 13 AB4 SER B 114 MET B 118 5 5 HELIX 14 AB5 PRO B 121 CYS B 126 5 5 SHEET 1 AA1 2 TYR A 75 VAL A 78 0 SHEET 2 AA1 2 ALA A 81 CYS A 84 -1 O VAL A 83 N LYS A 76 SHEET 1 AA2 2 TYR B 75 VAL B 78 0 SHEET 2 AA2 2 ALA B 81 CYS B 84 -1 O VAL B 83 N LYS B 76 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.00 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.02 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.06 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.02 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.06 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.00 SSBOND 8 CYS B 27 CYS B 126 1555 1555 2.05 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.05 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.05 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.04 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.03 SSBOND 13 CYS B 61 CYS B 91 1555 1555 2.02 SSBOND 14 CYS B 84 CYS B 96 1555 1555 1.99 CISPEP 1 ILE A 19 PRO A 20 0 23.09 CISPEP 2 ILE B 19 PRO B 20 0 11.85 CRYST1 76.825 90.375 77.590 90.00 90.00 90.00 C 2 2 21 16 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 0.013017 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012888 0.00000