HEADER HYDROLASE 16-APR-09 2WG7 TITLE STRUCTURE OF ORYZA SATIVA (RICE) PLA2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PHOSPHOLIPASE A2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PLA2; COMPND 5 EC: 3.1.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYZA SATIVA; SOURCE 3 ORGANISM_COMMON: RICE; SOURCE 4 ORGANISM_TAXID: 4530; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TUNER (DE3) KEYWDS HYDROLASE, SECRETORY PLA2 EXPDTA X-RAY DIFFRACTION AUTHOR J.E.GUY,U.STAHL,Y.LINDQVIST REVDAT 4 08-MAY-19 2WG7 1 REMARK REVDAT 3 06-MAR-19 2WG7 1 REMARK REVDAT 2 21-JUL-09 2WG7 1 JRNL REVDAT 1 02-JUN-09 2WG7 0 JRNL AUTH J.E.GUY,U.STAHL,Y.LINDQVIST JRNL TITL CRYSTAL STRUCTURE OF A CLASS XIB PHOSPHOLIPASE A2 (PLA2): JRNL TITL 2 RICE (ORYZA SATIVA) ISOFORM-2 PLA2 AND AN OCTANOATE COMPLEX. JRNL REF J.BIOL.CHEM. V. 284 19371 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19457861 JRNL DOI 10.1074/JBC.M109.008466 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18175 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 986 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1284 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1801 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -0.83000 REMARK 3 B12 (A**2) : 0.28000 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): 0.167 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.408 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1870 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2542 ; 1.021 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 4.372 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;32.039 ;24.458 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 311 ;11.823 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ; 8.951 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 286 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1414 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 845 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1303 ; 0.289 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 127 ; 0.142 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.098 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.149 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.148 ; 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): 1202 ; 0.568 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1931 ; 1.104 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 676 ; 1.511 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 606 ; 2.516 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 125 4 REMARK 3 1 B 2 B 125 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 880 ; 0.25 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 880 ; 0.25 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 880 ; 0.42 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 880 ; 0.42 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2WG7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-09. REMARK 100 THE DEPOSITION ID IS D_1290039485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : ID23-2; BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873; 1.771 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18175 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9100 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, MOLREP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: THIS IS THE HIGHER RESOLUTION STRUCTURE WHICH WAS SOLVED REMARK 200 BY MR FROM AN INITIAL S-SAD MODEL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION, 20 DEGREES WELL REMARK 280 CONTAINED 0.75ML OF SOLUTION A (16-18% PEG3350, 0.1M REMARK 280 BISTRISPROPANE PH 6.5, 0.2M POTASSIUM THIOCYANATE) AND 0.25ML REMARK 280 SOLUTION B (0.1M SODIUM ACETATE PH 4.6, 2M SODIUM CHLORIDE), REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 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 27.76800 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 13.88400 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 27.76800 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 13.88400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 LEU A 1 REMARK 465 SER A 9 REMARK 465 THR A 10 REMARK 465 PRO A 11 REMARK 465 ASP A 126 REMARK 465 GLY A 127 REMARK 465 GLN A 128 REMARK 465 MET B -1 REMARK 465 GLY B 0 REMARK 465 LEU B 1 REMARK 465 GLY B 8 REMARK 465 SER B 9 REMARK 465 THR B 10 REMARK 465 PRO B 11 REMARK 465 ALA B 12 REMARK 465 ASP B 126 REMARK 465 GLY B 127 REMARK 465 GLN B 128 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 14 32.07 -93.99 REMARK 500 SER A 23 72.23 -155.88 REMARK 500 HIS A 68 52.41 -116.52 REMARK 500 HIS A 68 51.67 -116.52 REMARK 500 SER B 23 77.80 -151.73 REMARK 500 ASP B 52 -168.44 -165.42 REMARK 500 REMARK 500 REMARK: NULL 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 A1126 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 37 O REMARK 620 2 ASP A 62 OD2 76.7 REMARK 620 3 TYR A 42 O 85.5 90.1 REMARK 620 4 ASP A 62 OD1 97.9 47.5 134.2 REMARK 620 5 HOH A2025 O 77.3 108.0 151.1 71.9 REMARK 620 6 GLY A 39 O 109.3 173.6 88.2 131.7 76.1 REMARK 620 7 HOH A2027 O 164.1 92.9 82.5 83.3 117.8 80.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1126 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2027 O REMARK 620 2 TYR B 42 O 80.6 REMARK 620 3 TYR B 37 O 162.2 87.9 REMARK 620 4 ASP B 62 OD1 75.8 127.8 101.2 REMARK 620 5 ASP B 62 OD2 88.0 85.4 77.5 48.4 REMARK 620 6 HOH B2025 O 112.6 155.2 83.2 76.8 114.9 REMARK 620 7 GLY B 39 O 80.5 85.7 112.3 133.6 166.5 76.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1127 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 89 OG REMARK 620 2 HOH A2032 O 82.6 REMARK 620 3 HOH A2034 O 165.9 102.8 REMARK 620 4 HOH A2035 O 77.6 90.2 89.2 REMARK 620 5 HOH B2064 O 84.1 162.9 92.6 97.4 REMARK 620 6 ARG B 87 O 100.2 83.4 93.4 173.5 88.3 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 CA A 1126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1127 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WG8 RELATED DB: PDB REMARK 900 STRUCTURE OF ORYZA SATIVA (RICE) PLA2, ORTHORHOMBIC CRYSTAL FORM REMARK 900 RELATED ID: 2WG9 RELATED DB: PDB REMARK 900 STRUCTURE OF ORYZA SATIVA (RICE) PLA2, COMPLEX WITH OCTANOIC ACID DBREF 2WG7 A -1 -1 PDB 2WG7 2WG7 -1 -1 DBREF 2WG7 A 0 128 UNP Q9XG81 Q9XG81_ORYSA 25 153 DBREF 2WG7 B -1 -1 PDB 2WG7 2WG7 -1 -1 DBREF 2WG7 B 0 128 UNP Q9XG81 Q9XG81_ORYSA 25 153 SEQRES 1 A 130 MET GLY LEU ASN ILE GLY ASP LEU LEU GLY SER THR PRO SEQRES 2 A 130 ALA LYS ASP GLN GLY CYS SER ARG THR CYS GLU SER GLN SEQRES 3 A 130 PHE CYS THR ILE ALA PRO LEU LEU ARG TYR GLY LYS TYR SEQRES 4 A 130 CYS GLY ILE LEU TYR SER GLY CYS PRO GLY GLU ARG PRO SEQRES 5 A 130 CYS ASP ALA LEU ASP ALA CYS CYS MET VAL HIS ASP HIS SEQRES 6 A 130 CYS VAL ASP THR HIS ASN ASP ASP TYR LEU ASN THR MET SEQRES 7 A 130 CYS ASN GLU ASN LEU LEU SER CYS ILE ASP ARG VAL SER SEQRES 8 A 130 GLY ALA THR PHE PRO GLY ASN LYS CYS ASN VAL GLY GLN SEQRES 9 A 130 THR ALA SER VAL ILE ARG GLY VAL ILE GLU THR ALA VAL SEQRES 10 A 130 PHE ALA GLY LYS ILE LEU HIS LYS ARG ASP ASP GLY GLN SEQRES 1 B 130 MET GLY LEU ASN ILE GLY ASP LEU LEU GLY SER THR PRO SEQRES 2 B 130 ALA LYS ASP GLN GLY CYS SER ARG THR CYS GLU SER GLN SEQRES 3 B 130 PHE CYS THR ILE ALA PRO LEU LEU ARG TYR GLY LYS TYR SEQRES 4 B 130 CYS GLY ILE LEU TYR SER GLY CYS PRO GLY GLU ARG PRO SEQRES 5 B 130 CYS ASP ALA LEU ASP ALA CYS CYS MET VAL HIS ASP HIS SEQRES 6 B 130 CYS VAL ASP THR HIS ASN ASP ASP TYR LEU ASN THR MET SEQRES 7 B 130 CYS ASN GLU ASN LEU LEU SER CYS ILE ASP ARG VAL SER SEQRES 8 B 130 GLY ALA THR PHE PRO GLY ASN LYS CYS ASN VAL GLY GLN SEQRES 9 B 130 THR ALA SER VAL ILE ARG GLY VAL ILE GLU THR ALA VAL SEQRES 10 B 130 PHE ALA GLY LYS ILE LEU HIS LYS ARG ASP ASP GLY GLN HET CA A1126 1 HET CA B1126 1 HET NA B1127 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 3 CA 2(CA 2+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *176(H2 O) HELIX 1 1 ASN A 2 LEU A 6 5 5 HELIX 2 2 ASP A 52 THR A 67 1 16 HELIX 3 3 ASN A 74 ASP A 86 1 13 HELIX 4 4 ASN A 99 ASP A 125 1 27 HELIX 5 5 ASN B 2 LEU B 7 5 6 HELIX 6 6 ASP B 52 THR B 67 1 16 HELIX 7 7 ASN B 74 ASP B 86 1 13 HELIX 8 8 ASN B 99 ASP B 125 1 27 SHEET 1 AA 2 GLU A 22 GLN A 24 0 SHEET 2 AA 2 ARG A 33 GLY A 35 -1 O ARG A 33 N GLN A 24 SHEET 1 BA 2 GLU B 22 GLN B 24 0 SHEET 2 BA 2 ARG B 33 GLY B 35 -1 O ARG B 33 N GLN B 24 SSBOND 1 CYS A 17 CYS A 45 1555 1555 2.04 SSBOND 2 CYS A 21 CYS A 51 1555 1555 2.04 SSBOND 3 CYS A 26 CYS A 98 1555 1555 2.03 SSBOND 4 CYS A 38 CYS A 58 1555 1555 2.04 SSBOND 5 CYS A 57 CYS A 84 1555 1555 2.04 SSBOND 6 CYS A 64 CYS A 77 1555 1555 2.05 SSBOND 7 CYS B 17 CYS B 45 1555 1555 2.03 SSBOND 8 CYS B 21 CYS B 51 1555 1555 2.04 SSBOND 9 CYS B 26 CYS B 98 1555 1555 2.03 SSBOND 10 CYS B 38 CYS B 58 1555 1555 2.06 SSBOND 11 CYS B 57 CYS B 84 1555 1555 2.03 SSBOND 12 CYS B 64 CYS B 77 1555 1555 2.04 LINK CA CA A1126 O TYR A 37 1555 1555 2.34 LINK CA CA A1126 OD2 ASP A 62 1555 1555 2.51 LINK CA CA A1126 O TYR A 42 1555 1555 2.27 LINK CA CA A1126 OD1 ASP A 62 1555 1555 2.84 LINK CA CA A1126 O HOH A2025 1555 1555 2.75 LINK CA CA A1126 O GLY A 39 1555 1555 2.50 LINK CA CA A1126 O HOH A2027 1555 1555 2.42 LINK CA CA B1126 O HOH B2027 1555 1555 2.46 LINK CA CA B1126 O TYR B 42 1555 1555 2.27 LINK CA CA B1126 O TYR B 37 1555 1555 2.28 LINK CA CA B1126 OD1 ASP B 62 1555 1555 2.70 LINK CA CA B1126 OD2 ASP B 62 1555 1555 2.63 LINK CA CA B1126 O HOH B2025 1555 1555 2.77 LINK CA CA B1126 O GLY B 39 1555 1555 2.54 LINK NA NA B1127 OG SER B 89 1555 1555 2.51 LINK NA NA B1127 O HOH A2032 1555 1555 2.54 LINK NA NA B1127 O HOH A2034 1555 1555 2.38 LINK NA NA B1127 O HOH A2035 1555 1555 2.51 LINK NA NA B1127 O HOH B2064 1555 1555 2.40 LINK NA NA B1127 O ARG B 87 1555 1555 2.33 CISPEP 1 LEU A 7 GLY A 8 0 0.82 SITE 1 AC1 6 TYR A 37 GLY A 39 TYR A 42 ASP A 62 SITE 2 AC1 6 HOH A2025 HOH A2027 SITE 1 AC2 6 TYR B 37 GLY B 39 TYR B 42 ASP B 62 SITE 2 AC2 6 HOH B2025 HOH B2027 SITE 1 AC3 6 HOH A2032 HOH A2034 HOH A2035 ARG B 87 SITE 2 AC3 6 SER B 89 HOH B2064 CRYST1 108.667 108.667 41.652 90.00 90.00 120.00 P 62 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 0.009202 0.005313 0.000000 0.00000 SCALE2 0.000000 0.010626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024008 0.00000