10 20 30 40 50 60 70 80 1SFV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 20-FEB-96 1SFV
TITLE PORCINE PANCREAS PHOSPHOLIPASE A2, NMR, MINIMIZED AVERAGE TITLE 2 STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PLA2, PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE; COMPND 5 EC: 3.1.1.4; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: THIS ENTRY PRESENTS THE SOLUTION STRUCTURE COMPND 8 OF THE ENZYME IN THE PRESENCE OF LIPID MICELLES AND A COMPND 9 COMPETITIVE INHIBITOR
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 ORGAN: PANCREAS; SOURCE 6 GENE: PORCINE PANCREAS PLA2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAB3 (PGEX T2 DERIVED SOURCE 10 EXPRESSION PLASMID); SOURCE 11 EXPRESSION_SYSTEM_GENE: PORCINE PANCREAS PLA2; SOURCE 12 OTHER_DETAILS: DETAILS CONCERNING THE EXPRESSION OF THE SOURCE 13 PLA2 CAN BE FOUND IN REFERENCES BELOW
KEYWDS PHOSPHOLIPASE A2, PHOSPHATIDE-2-ACYL-HYDROLASE
EXPDTA SOLUTION NMR
AUTHOR B.VAN DEN BERG,M.TESSARI,R.BOELENS,R.DIJKMAN,R.KAPTEIN, AUTHOR 2 G.H.DE HAAS,H.M.VERHEIJ
REVDAT 3 24-FEB-09 1SFV 1 VERSN REVDAT 2 01-APR-03 1SFV 1 JRNL REVDAT 1 11-JUL-96 1SFV 0
JRNL AUTH B.VAN DEN BERG,M.TESSARI,R.BOELENS,R.DIJKMAN, JRNL AUTH 2 R.KAPTEIN,G.H.DE HAAS,H.M.VERHEIJ JRNL TITL SOLUTION STRUCTURE OF PORCINE PANCREATIC JRNL TITL 2 PHOSPHOLIPASE A2 COMPLEXED WITH MICELLES AND A JRNL TITL 3 COMPETITIVE INHIBITOR. JRNL REF J.BIOMOL.NMR V. 5 110 1995 JRNL REFN ISSN 0925-2738 JRNL PMID 7703697 JRNL DOI 10.1007/BF00208802
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.VAN DEN BERG,M.TESSARI,G.H.DE HAAS,H.M.VERHEIJ, REMARK 1 AUTH 2 R.BOELENS,R.KAPTEIN REMARK 1 TITL SOLUTION STRUCTURE OF PORCINE PANCREATIC REMARK 1 TITL 2 PHOSPHOLIPASE A2 REMARK 1 REF EMBO J. V. 14 4123 1995 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.VAN DEN BERG,M.TESSARI,R.BOELENS,R.DIJKMAN, REMARK 1 AUTH 2 G.H.DE HAAS,R.KAPTEIN,H.M.VERHEIJ REMARK 1 TITL NMR STRUCTURES OF PHOSPHOLIPASE A2 REVEAL REMARK 1 TITL 2 CONFORMATIONAL CHANGES DURING INTERFACIAL REMARK 1 TITL 3 ACTIVATION REMARK 1 REF NAT.STRUCT.BIOL. V. 2 402 1995 REMARK 1 REFN ISSN 1072-8368
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : BIOSYM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1SFV COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL
REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 40 CD GLU A 40 OE1 0.120 REMARK 500 GLU A 46 CD GLU A 46 OE1 0.119 REMARK 500 HIS A 48 CG HIS A 48 CD2 0.058 REMARK 500 GLU A 71 CD GLU A 71 OE2 0.120 REMARK 500 GLU A 81 CD GLU A 81 OE1 0.120 REMARK 500 GLU A 92 CD GLU A 92 OE2 0.118 REMARK 500 GLU A 114 CD GLU A 114 OE2 0.120 REMARK 500 CYS A 124 C CYS A 124 OXT 0.145 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 HIS A 17 CB - CG - CD2 ANGL. DEV. = -11.8 DEGREES REMARK 500 HIS A 17 CG - ND1 - CE1 ANGL. DEV. = -8.1 DEGREES REMARK 500 HIS A 17 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 MET A 20 N - CA - CB ANGL. DEV. = -12.4 DEGREES REMARK 500 ASP A 21 CB - CG - OD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 TYR A 28 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR A 28 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 LEU A 31 CB - CA - C ANGL. DEV. = 13.5 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 42 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 HIS A 48 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 49 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 54 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 59 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 LEU A 64 CB - CG - CD2 ANGL. DEV. = -10.6 DEGREES REMARK 500 ASP A 66 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 TYR A 69 CB - CG - CD1 ANGL. DEV. = 4.1 DEGREES REMARK 500 SER A 72 N - CA - CB ANGL. DEV. = -9.5 DEGREES REMARK 500 TYR A 73 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 TYR A 75 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 TYR A 75 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR A 75 CB - CG - CD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ILE A 82 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 CYS A 84 N - CA - CB ANGL. DEV. = 11.8 DEGREES REMARK 500 ASP A 99 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 100 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 PHE A 106 CB - CG - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 PHE A 106 CB - CG - CD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 TYR A 111 CB - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TYR A 111 CB - CG - CD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 GLU A 114 CB - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 HIS A 115 CB - CG - CD2 ANGL. DEV. = -12.5 DEGREES REMARK 500 HIS A 115 ND1 - CE1 - NE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 LYS A 116 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 LYS A 122 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 TYR A 123 N - CA - CB ANGL. DEV. = -20.1 DEGREES REMARK 500 TYR A 123 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES 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 2 -60.56 -93.55 REMARK 500 SER A 16 -91.96 -157.40 REMARK 500 LEU A 19 -116.98 -72.16 REMARK 500 MET A 20 -28.09 4.31 REMARK 500 ASP A 21 -4.44 -56.46 REMARK 500 PHE A 22 -46.29 -139.66 REMARK 500 TYR A 25 107.44 -168.69 REMARK 500 TYR A 28 -28.29 -160.15 REMARK 500 CYS A 29 111.57 -10.85 REMARK 500 LEU A 31 -82.33 -102.63 REMARK 500 PRO A 37 -154.05 -88.88 REMARK 500 VAL A 38 -59.06 -131.89 REMARK 500 ASP A 49 -60.73 165.58 REMARK 500 LEU A 58 139.70 -5.80 REMARK 500 PHE A 63 -125.04 -150.48 REMARK 500 LEU A 64 -62.28 -92.14 REMARK 500 ASN A 67 -80.93 -116.08 REMARK 500 THR A 70 -46.67 -175.19 REMARK 500 TYR A 73 134.09 113.44 REMARK 500 SER A 74 82.73 -176.23 REMARK 500 TYR A 75 -137.64 -119.78 REMARK 500 SER A 76 -179.25 -171.06 REMARK 500 SER A 78 -128.08 -103.94 REMARK 500 THR A 80 -30.86 -174.98 REMARK 500 ILE A 82 -115.83 -114.76 REMARK 500 THR A 83 -101.34 -173.74 REMARK 500 CYS A 84 -69.31 177.24 REMARK 500 SER A 86 58.57 -145.87 REMARK 500 LYS A 87 -62.01 -160.05 REMARK 500 ASN A 88 127.28 55.77 REMARK 500 ASN A 89 -123.13 -129.25 REMARK 500 CYS A 91 -61.47 -16.16 REMARK 500 LYS A 108 -73.49 -138.16 REMARK 500 ALA A 109 -166.75 30.77 REMARK 500 GLU A 114 -57.67 -152.77 REMARK 500 ASN A 117 -46.62 93.60 REMARK 500 LEU A 118 -151.07 25.86 REMARK 500 ASP A 119 -44.50 -170.35 REMARK 500 THR A 120 60.20 90.31 REMARK 500 LYS A 121 -69.48 -151.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 14 GLY A 15 123.85 REMARK 500 MET A 20 ASP A 21 134.15 REMARK 500 LEU A 64 VAL A 65 -143.37 REMARK 500 SER A 76 CYS A 77 140.70 REMARK 500 ASN A 88 ASN A 89 148.33 REMARK 500 LYS A 113 GLU A 114 -136.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 22 0.08 SIDE_CHAIN REMARK 500 TYR A 25 0.13 SIDE_CHAIN REMARK 500 TYR A 28 0.09 SIDE_CHAIN REMARK 500 TYR A 52 0.10 SIDE_CHAIN REMARK 500 TYR A 69 0.11 SIDE_CHAIN REMARK 500 TYR A 73 0.14 SIDE_CHAIN REMARK 500 TYR A 75 0.08 SIDE_CHAIN REMARK 500 HIS A 115 0.22 SIDE_CHAIN REMARK 500 TYR A 123 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: CATALYTIC CALCIUM ION (COFACTOR). REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 125
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SFW RELATED DB: PDB
DBREF 1SFV A 1 124 UNP P00592 PA21B_PIG 23 146
SEQRES 1 A 124 ALA LEU TRP GLN PHE ARG SER MET ILE LYS CYS ALA ILE SEQRES 2 A 124 PRO GLY SER HIS PRO LEU MET ASP PHE ASN ASN TYR GLY SEQRES 3 A 124 CYS TYR CYS GLY LEU GLY GLY SER GLY THR PRO VAL ASP SEQRES 4 A 124 GLU LEU ASP ARG CYS CYS GLU THR HIS ASP ASN CYS TYR SEQRES 5 A 124 ARG ASP ALA LYS ASN LEU ASP SER CYS LYS PHE LEU VAL SEQRES 6 A 124 ASP ASN PRO TYR THR GLU SER TYR SER TYR SER CYS SER SEQRES 7 A 124 ASN THR GLU ILE THR CYS ASN SER LYS ASN ASN ALA CYS SEQRES 8 A 124 GLU ALA PHE ILE CYS ASN CYS ASP ARG ASN ALA ALA ILE SEQRES 9 A 124 CYS PHE SER LYS ALA PRO TYR ASN LYS GLU HIS LYS ASN SEQRES 10 A 124 LEU ASP THR LYS LYS TYR CYS
HET CA A 125 1
HETNAM CA CALCIUM ION
FORMUL 2 CA CA 2+
HELIX 1 1 LEU A 2 ALA A 12 1 11 HELIX 2 2 GLU A 40 ASN A 50 1 11 HELIX 3 3 ARG A 53 ALA A 55 5 3 HELIX 4 4 ALA A 93 PHE A 106 1 14
SSBOND 1 CYS A 11 CYS A 77 1555 1555 2.00 SSBOND 2 CYS A 27 CYS A 124 1555 1555 1.97 SSBOND 3 CYS A 29 CYS A 45 1555 1555 1.99 SSBOND 4 CYS A 44 CYS A 105 1555 1555 1.99 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.00 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.02 SSBOND 7 CYS A 84 CYS A 96 1555 1555 1.98
LINK CA CA A 125 OD2 ASP A 49 1555 1555 3.16
SITE 1 CA 1 CA A 125 SITE 1 AC1 4 GLY A 30 LEU A 31 CYS A 45 ASP A 49
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000