10 20 30 40 50 60 70 80 1Y6O - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 06-DEC-04 1Y6O
TITLE CRYSTAL STRUCTURE OF DISULFIDE ENGINEERED PORCINE PANCREATIC TITLE 2 PHOSPHOLIPASE A2 TO GROUP-X ISOZYME IN COMPLEX WITH INHIBITOR MJ33 TITLE 3 AND PHOSPHATE IONS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2, MAJOR ISOENZYME; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE COMPND 5 A2; COMPND 6 EC: 3.1.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: M8L,M20L, N50C, C-TERMIAL INSERTION KGESDKC (RESIDUES COMPND 10 125 TO 131)
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 GENE: PLA2G1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PC2429; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMAR25
KEYWDS HYDROLASE. DISULFIDE ENGINEERED PLA2. PORCINE PANCRATIC ISOZYME., KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR B.Z.YU,Y.H.PAN,M.J.W.JASSEN,B.J.BAHNSON,M.K.JAIN
REVDAT 3 13-JUL-11 1Y6O 1 VERSN REVDAT 2 24-FEB-09 1Y6O 1 VERSN REVDAT 1 22-MAR-05 1Y6O 0
JRNL AUTH B.Z.YU,Y.H.PAN,M.J.W.JANSSEN,B.J.BAHNSON,M.K.JAIN JRNL TITL KINETIC AND STRUCTURAL PROPERTIES OF DISULFIDE ENGINEERED JRNL TITL 2 PHOSPHOLIPASE A(2): INSIGHT INTO THE ROLE OF DISULFIDE JRNL TITL 3 BONDING PATTERNS. JRNL REF BIOCHEMISTRY V. 44 3369 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15736947 JRNL DOI 10.1021/BI0482147
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.JANSSEN,H.M.VERHEIJ,A.J.SLOTBOOM,M.R.EGMOND REMARK 1 TITL ENGINEEERING THE DISULPHIDE BOND PATTERNS OF SECRETORY REMARK 1 TITL 2 PHOSPOLIPASES A2 INTO PORCINE PANCRATIC ISOZYME. THE EFFECTS REMARK 1 TITL 3 ON FOLDING, STABILITY AND ENZYMATIC PROPERTIES REMARK 1 REF EUR.J.BIOCHEM. V. 261 197 1999 REMARK 1 REFN ISSN 0014-2956 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.H.PAN,B.Z.YU,A.G.SINGER,F.GHOMASHCHI,G.LAMBEAU,M.K.JAIN, REMARK 1 AUTH 2 B.J.BAHNSON REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN GROUP X SECRETED PHOSPHOLIPASE REMARK 1 TITL 2 A2. ELECTROSTATICALLY NEUTRAL INTERFACIAL SURFACE TARGETS REMARK 1 TITL 3 ZWITTERIONIC MEMBRANES REMARK 1 REF J.MOL.BIOL. V. 277 29086 2002 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 427212.240 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.8 REMARK 3 NUMBER OF REFLECTIONS : 14222 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 SET) : 0.196 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 717 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2057 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 98 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2040 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.79000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : -0.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.27000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.71 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.010 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.590 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.730 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.470 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 49.22 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : MY_TOPPAR:MJ33_13.PAR REMARK 3 PARAMETER FILE 5 : MY_TOPPAR:MJ33_C11.PAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : MY_TOPPAR:MJ33_C13.TOP REMARK 3 TOPOLOGY FILE 5 : MY_TOPPAR:MJ33_C11.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ATOMS C2-C16 IN RESIDUE 217 AND ATOMS REMARK 3 C4-C16 IN RESIDUE 218 WERE DELETED FROM THE MODEL DUE TO DISORDER.
REMARK 4 REMARK 4 1Y6O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-04. REMARK 100 THE RCSB ID CODE IS RCSB031183.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 93 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS 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 : 14222 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.31600 REMARK 200 R SYM FOR SHELL (I) : 0.29300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FXF REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM PHOSPHATE, PEG 8000, , PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 42.96050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS TWO BIOLOGICAL UNITS: CHAIN A REMARK 300 AND B.
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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -87.0 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 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 CYS A 61 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 CYS B 61 CA - CB - SG ANGL. DEV. = 6.8 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 ASP A 39 -179.08 -171.73 REMARK 500 LYS A 62 -67.54 -18.38 REMARK 500 ASP B 39 -178.26 -171.71 REMARK 500 LYS B 62 -75.00 -10.63 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 302 DISTANCE = 8.78 ANGSTROMS
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MJI A 217 REMARK 610 MJI B 218
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 CA A 207 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 30 O REMARK 620 2 ASP A 49 OD1 143.7 REMARK 620 3 HOH A 218 O 79.6 85.5 REMARK 620 4 GLY A 32 O 83.2 128.1 84.3 REMARK 620 5 ASP A 49 OD2 162.1 51.3 95.0 79.2 REMARK 620 6 MJI A 217 O21 69.9 80.8 100.5 151.1 128.0 REMARK 620 7 TYR A 28 O 91.4 100.7 170.6 97.2 94.4 73.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 208 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 49 OD1 REMARK 620 2 ASP B 49 OD2 50.5 REMARK 620 3 GLY B 30 O 139.9 166.0 REMARK 620 4 GLY B 32 O 132.2 85.0 81.8 REMARK 620 5 HOH B 228 O 78.6 90.9 83.9 87.0 REMARK 620 6 MJI B 218 O21 77.7 122.2 71.7 150.1 103.4 REMARK 620 7 TYR B 28 O 104.5 93.5 91.6 93.1 175.5 74.4 REMARK 620 N 1 2 3 4 5 6
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 211 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MJI A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MJI B 218
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y6P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DISULFIDE ENGINEERED PORCINE PANCRATIC REMARK 900 PHOSPHOLIPASE A2 GROUP X ISOZYME REMARK 900 RELATED ID: 1FXF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PORCINE PANCRATIC PHOSPHOLIPASE A2 REMARK 900 (GROUP 1B) IN COMPLEX WITH INHIBITOR MJ33 AND PHOSPHATE IONS REMARK 900 RELATED ID: 1LE6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN GROUP X SECRETED PHOSPHOLIPASE REMARK 900 A2 (SPLA2)
REMARK 999 REMARK 999 SEQUENCE C-TERMINAL EXTENSION (RESIDUES 125-131) KGESDKC WERE ADDED REMARK 999 TO MODEL THE DISULFIDE BONDING PATTERN OF THE GROUP X ENZYME.
DBREF 1Y6O A 1 124 UNP P00592 PA21B_PIG 23 146 DBREF 1Y6O B 1 124 UNP P00592 PA21B_PIG 23 146
SEQADV 1Y6O LEU A 8 UNP P00592 MET 30 ENGINEERED SEQADV 1Y6O LEU A 20 UNP P00592 MET 42 ENGINEERED SEQADV 1Y6O CYS A 50 UNP P00592 ASN 72 ENGINEERED SEQADV 1Y6O LYS A 125 UNP P00592 SEE REMARK 999 SEQADV 1Y6O GLY A 126 UNP P00592 SEE REMARK 999 SEQADV 1Y6O GLU A 127 UNP P00592 SEE REMARK 999 SEQADV 1Y6O SER A 128 UNP P00592 SEE REMARK 999 SEQADV 1Y6O ASP A 129 UNP P00592 SEE REMARK 999 SEQADV 1Y6O LYS A 130 UNP P00592 SEE REMARK 999 SEQADV 1Y6O CYS A 131 UNP P00592 SEE REMARK 999 SEQADV 1Y6O LEU B 8 UNP P00592 MET 30 ENGINEERED SEQADV 1Y6O LEU B 20 UNP P00592 MET 42 ENGINEERED SEQADV 1Y6O CYS B 50 UNP P00592 ASN 72 ENGINEERED SEQADV 1Y6O LYS B 125 UNP P00592 SEE REMARK 999 SEQADV 1Y6O GLY B 126 UNP P00592 SEE REMARK 999 SEQADV 1Y6O GLU B 127 UNP P00592 SEE REMARK 999 SEQADV 1Y6O SER B 128 UNP P00592 SEE REMARK 999 SEQADV 1Y6O ASP B 129 UNP P00592 SEE REMARK 999 SEQADV 1Y6O LYS B 130 UNP P00592 SEE REMARK 999 SEQADV 1Y6O CYS B 131 UNP P00592 SEE REMARK 999
SEQRES 1 A 131 ALA LEU TRP GLN PHE ARG SER LEU ILE LYS CYS ALA ILE SEQRES 2 A 131 PRO GLY SER HIS PRO LEU LEU ASP PHE ASN ASN TYR GLY SEQRES 3 A 131 CYS TYR CYS GLY LEU GLY GLY SER GLY THR PRO VAL ASP SEQRES 4 A 131 GLU LEU ASP ARG CYS CYS GLU THR HIS ASP CYS CYS TYR SEQRES 5 A 131 ARG ASP ALA LYS ASN LEU ASP SER CYS LYS PHE LEU VAL SEQRES 6 A 131 ASP ASN PRO TYR THR GLU SER TYR SER TYR SER CYS SER SEQRES 7 A 131 ASN THR GLU ILE THR CYS ASN SER LYS ASN ASN ALA CYS SEQRES 8 A 131 GLU ALA PHE ILE CYS ASN CYS ASP ARG ASN ALA ALA ILE SEQRES 9 A 131 CYS PHE SER LYS ALA PRO TYR ASN LYS GLU HIS LYS ASN SEQRES 10 A 131 LEU ASP THR LYS LYS TYR CYS LYS GLY GLU SER ASP LYS SEQRES 11 A 131 CYS SEQRES 1 B 131 ALA LEU TRP GLN PHE ARG SER LEU ILE LYS CYS ALA ILE SEQRES 2 B 131 PRO GLY SER HIS PRO LEU LEU ASP PHE ASN ASN TYR GLY SEQRES 3 B 131 CYS TYR CYS GLY LEU GLY GLY SER GLY THR PRO VAL ASP SEQRES 4 B 131 GLU LEU ASP ARG CYS CYS GLU THR HIS ASP CYS CYS TYR SEQRES 5 B 131 ARG ASP ALA LYS ASN LEU ASP SER CYS LYS PHE LEU VAL SEQRES 6 B 131 ASP ASN PRO TYR THR GLU SER TYR SER TYR SER CYS SER SEQRES 7 B 131 ASN THR GLU ILE THR CYS ASN SER LYS ASN ASN ALA CYS SEQRES 8 B 131 GLU ALA PHE ILE CYS ASN CYS ASP ARG ASN ALA ALA ILE SEQRES 9 B 131 CYS PHE SER LYS ALA PRO TYR ASN LYS GLU HIS LYS ASN SEQRES 10 B 131 LEU ASP THR LYS LYS TYR CYS LYS GLY GLU SER ASP LYS SEQRES 11 B 131 CYS
HET CA A 207 1 HET CA B 208 1 HET PO4 A 209 5 HET PO4 B 210 5 HET PO4 A 211 5 HET PO4 A 212 5 HET PO4 A 213 5 HET PO4 B 214 5 HET PO4 A 215 5 HET PO4 B 216 5 HET MJI A 217 17 HET MJI B 218 19
HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION HETNAM MJI 1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATE HETNAM 2 MJI METHANE
HETSYN MJI MJ33 INHIBITOR
FORMUL 3 CA 2(CA 2+) FORMUL 5 PO4 8(O4 P 3-) FORMUL 13 MJI 2(C22 H44 F3 O6 P) FORMUL 15 HOH *206(H2 O)
HELIX 1 1 ALA A 1 ILE A 13 1 13 HELIX 2 2 HIS A 17 PHE A 22 1 6 HELIX 3 3 ASP A 39 ASN A 57 1 19 HELIX 4 4 ASN A 67 GLU A 71 5 5 HELIX 5 5 ASN A 89 ALA A 109 1 21 HELIX 6 6 ASN A 112 LYS A 116 5 5 HELIX 7 7 ASP A 119 CYS A 124 1 6 HELIX 8 8 ALA B 1 ILE B 13 1 13 HELIX 9 9 HIS B 17 ASN B 23 1 7 HELIX 10 10 ASP B 39 ASN B 57 1 19 HELIX 11 11 ASN B 67 GLU B 71 5 5 HELIX 12 12 ASN B 89 ALA B 109 1 21 HELIX 13 13 ASN B 112 LYS B 116 5 5 HELIX 14 14 ASP B 119 CYS B 124 1 6
SHEET 1 A 2 TYR A 75 SER A 78 0 SHEET 2 A 2 GLU A 81 CYS A 84 -1 O GLU A 81 N SER A 78 SHEET 1 B 2 TYR B 75 SER B 78 0 SHEET 2 B 2 GLU B 81 CYS B 84 -1 O GLU B 81 N SER B 78
SSBOND 1 CYS A 11 CYS A 77 1555 1555 2.03 SSBOND 2 CYS A 27 CYS A 124 1555 1555 2.03 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 4 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 5 CYS A 50 CYS A 131 1555 1555 2.03 SSBOND 6 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 7 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 8 CYS A 84 CYS A 96 1555 1555 2.03 SSBOND 9 CYS B 11 CYS B 77 1555 1555 2.03 SSBOND 10 CYS B 27 CYS B 124 1555 1555 2.03 SSBOND 11 CYS B 29 CYS B 45 1555 1555 2.03 SSBOND 12 CYS B 44 CYS B 105 1555 1555 2.03 SSBOND 13 CYS B 50 CYS B 131 1555 1555 2.03 SSBOND 14 CYS B 51 CYS B 98 1555 1555 2.03 SSBOND 15 CYS B 61 CYS B 91 1555 1555 2.03 SSBOND 16 CYS B 84 CYS B 96 1555 1555 2.03
LINK CA CA A 207 O GLY A 30 1555 1555 2.27 LINK CA CA A 207 OD1 ASP A 49 1555 1555 2.60 LINK CA CA A 207 O HOH A 218 1555 1555 2.29 LINK CA CA A 207 O GLY A 32 1555 1555 2.39 LINK CA CA A 207 OD2 ASP A 49 1555 1555 2.46 LINK CA CA A 207 O21 MJI A 217 1555 1555 2.69 LINK CA CA A 207 O TYR A 28 1555 1555 2.37 LINK CA CA B 208 OD1 ASP B 49 1555 1555 2.64 LINK CA CA B 208 OD2 ASP B 49 1555 1555 2.50 LINK CA CA B 208 O GLY B 30 1555 1555 2.22 LINK CA CA B 208 O GLY B 32 1555 1555 2.45 LINK CA CA B 208 O HOH B 228 1555 1555 2.41 LINK CA CA B 208 O21 MJI B 218 1555 1555 2.50 LINK CA CA B 208 O TYR B 28 1555 1555 2.35
SITE 1 AC1 6 TYR A 28 GLY A 30 GLY A 32 ASP A 49 SITE 2 AC1 6 MJI A 217 HOH A 218 SITE 1 AC2 6 TYR B 28 GLY B 30 GLY B 32 ASP B 49 SITE 2 AC2 6 MJI B 218 HOH B 228 SITE 1 AC3 8 ARG A 6 HIS A 17 PRO A 18 LEU A 19 SITE 2 AC3 8 LEU A 20 HOH A 309 HOH A 312 ARG B 6 SITE 1 AC4 9 ARG A 6 PO4 A 211 ARG B 6 HIS B 17 SITE 2 AC4 9 PRO B 18 LEU B 19 LEU B 20 HOH B 220 SITE 3 AC4 9 HOH B 222 SITE 1 AC5 8 ARG A 6 LYS A 10 LYS A 122 LYS A 125 SITE 2 AC5 8 HOH A 321 ARG B 6 HIS B 17 PO4 B 210 SITE 1 AC6 3 ARG A 43 HOH A 277 HOH A 315 SITE 1 AC7 6 ASP A 39 GLU A 40 PRO A 110 ASN A 112 SITE 2 AC7 6 HOH A 238 HOH A 286 SITE 1 AC8 6 ASP B 39 GLU B 40 PRO B 110 ASN B 112 SITE 2 AC8 6 HOH B 244 HOH B 246 SITE 1 AC9 7 ASP A 21 LYS A 62 PHE A 63 ASP A 66 SITE 2 AC9 7 TYR A 111 HOH A 322 LYS B 121 SITE 1 BC1 7 LYS A 121 ASP B 21 LYS B 62 PHE B 63 SITE 2 BC1 7 ASP B 66 TYR B 111 LYS B 113 SITE 1 BC2 14 LEU A 2 PHE A 5 PRO A 18 LEU A 19 SITE 2 BC2 14 ASN A 23 TYR A 28 GLY A 30 LEU A 31 SITE 3 BC2 14 ASP A 49 TYR A 69 CA A 207 HOH A 219 SITE 4 BC2 14 HOH A 285 MJI B 218 SITE 1 BC3 13 MJI A 217 PHE B 5 ILE B 9 PRO B 18 SITE 2 BC3 13 LEU B 19 ASN B 23 TYR B 28 GLY B 30 SITE 3 BC3 13 LEU B 31 ASP B 49 TYR B 69 CA B 208 SITE 4 BC3 13 HOH B 309
CRYST1 38.534 85.921 38.554 90.00 94.76 90.00 P 1 21 1 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 0.025951 0.000000 0.002160 0.00000
SCALE2 0.000000 0.011639 0.000000 0.00000
SCALE3 0.000000 0.000000 0.026027 0.00000