HEADER HYDROLASE 08-SEP-09 3JR8 TITLE CRYSTAL STRUCTURE OF BTHTX-II (ASP49-PLA2 FROM BOTHROPS JARARACUSSU TITLE 2 SNAKE VENOM) WITH CALCIUM IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2 BOTHROPSTOXIN-2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, MYOTOXIC PHOSPHOLIPASE COMPND 5 A2, BOTHROPSTOXIN II, BTHTX-II, BTXTXII, BOJU-II, BJU-PLA2, BJUPLA2; COMPND 6 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS JARARACUSSU; SOURCE 3 ORGANISM_TAXID: 8726; SOURCE 4 SECRETION: VENOM KEYWDS PHOSPHOLIPASES A2, ASP49-PLA2, MIOTOXIC ASP49-PLA2, BOTHROPSTOXIN II, KEYWDS 2 BTHTX-II, DISULFIDE BOND, HYDROLASE, LIPID DEGRADATION, METAL- KEYWDS 3 BINDING, SECRETED EXPDTA X-RAY DIFFRACTION AUTHOR R.J.BORGES,J.I.DOS SANTOS,M.R.M.FONTES REVDAT 3 06-SEP-23 3JR8 1 REMARK LINK REVDAT 2 26-JUN-13 3JR8 1 JRNL VERSN REVDAT 1 08-SEP-10 3JR8 0 JRNL AUTH J.I.DOS SANTOS,M.CINTRA-FRANCISCHINELLI,R.J.BORGES, JRNL AUTH 2 C.A.FERNANDES,P.PIZZO,A.C.CINTRA,A.S.BRAZ,A.M.SOARES, JRNL AUTH 3 M.R.FONTES JRNL TITL STRUCTURAL, FUNCTIONAL, AND BIOINFORMATICS STUDIES REVEAL A JRNL TITL 2 NEW SNAKE VENOM HOMOLOGUE PHOSPHOLIPASE A2 CLASS. JRNL REF PROTEINS V. 79 61 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 20878713 JRNL DOI 10.1002/PROT.22858 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 12101 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 614 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 893 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.3040 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.4090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 88 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : -1.11000 REMARK 3 B33 (A**2) : 3.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.78000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.162 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.129 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1956 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2656 ; 1.673 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 242 ; 6.591 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;39.310 ;23.647 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;21.086 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.928 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 265 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1514 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 980 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1315 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 113 ; 0.186 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 46 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.282 ; 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): 1212 ; 1.299 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1932 ; 1.953 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 744 ; 3.070 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 724 ; 4.137 ; 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): 1956 ; 1.725 ; 3.000 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 : NULL 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 : 1.40 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 3JR8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055057. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.425 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13058 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.550 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 2OQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, PEG 4000, SODIUM CITRATE, REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.61800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.43950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.61800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 50.43950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 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 REMARK 350 BIOMOLECULE: 2 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: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 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 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 138 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 150 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 43 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 GLU A 78 CG CD OE1 OE2 REMARK 470 ILE A 82 CG1 CG2 CD1 REMARK 470 GLU A 86 CG CD OE1 OE2 REMARK 470 LYS A 114 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 ASP A 122 CG OD1 OD2 REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 LYS A 132 CG CD CE NZ REMARK 470 ARG B 111 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 115 CG CD CE NZ 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 66.30 -101.48 REMARK 500 ALA A 130 -48.25 -131.05 REMARK 500 GLU B 78 11.38 -59.79 REMARK 500 VAL B 124 1.94 -58.41 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 A 134 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 22 OH REMARK 620 2 THR A 41 OG1 140.6 REMARK 620 3 PHE A 106 O 95.8 111.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 135 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 39 OD2 REMARK 620 2 THR A 41 OG1 112.1 REMARK 620 3 THR A 112 OG1 116.0 130.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 134 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR B 22 OH REMARK 620 2 THR B 41 OG1 132.1 REMARK 620 3 PHE B 106 O 97.3 121.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 135 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 39 OD2 REMARK 620 2 THR B 41 OG1 109.5 REMARK 620 3 THR B 112 OG1 119.6 123.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 134 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 135 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OQD RELATED DB: PDB REMARK 900 THE SAME PROTEIN BUT NATIVE REMARK 900 RELATED ID: 1GMZ RELATED DB: PDB REMARK 900 PIRATOXIN III (MIOTOXIC ASP49-PLA2) DBREF 3JR8 A 1 133 UNP P45881 PA2B2_BOTJR 17 138 DBREF 3JR8 B 1 133 UNP P45881 PA2B2_BOTJR 17 138 SEQRES 1 A 122 ASP LEU TRP GLN PHE GLY GLN MET ILE LEU LYS GLU THR SEQRES 2 A 122 GLY LYS LEU PRO PHE PRO TYR TYR THR THR TYR GLY CYS SEQRES 3 A 122 TYR CYS GLY TRP GLY GLY GLN GLY GLN PRO LYS ASP ALA SEQRES 4 A 122 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 A 122 LYS LEU THR ASN CYS LYS PRO LYS THR ASP ARG TYR SER SEQRES 6 A 122 TYR SER ARG GLU ASN GLY VAL ILE ILE CYS GLY GLU GLY SEQRES 7 A 122 THR PRO CYS GLU LYS GLN ILE CYS GLU CYS ASP LYS ALA SEQRES 8 A 122 ALA ALA VAL CYS PHE ARG GLU ASN LEU ARG THR TYR LYS SEQRES 9 A 122 LYS ARG TYR MET ALA TYR PRO ASP VAL LEU CYS LYS LYS SEQRES 10 A 122 PRO ALA GLU LYS CYS SEQRES 1 B 122 ASP LEU TRP GLN PHE GLY GLN MET ILE LEU LYS GLU THR SEQRES 2 B 122 GLY LYS LEU PRO PHE PRO TYR TYR THR THR TYR GLY CYS SEQRES 3 B 122 TYR CYS GLY TRP GLY GLY GLN GLY GLN PRO LYS ASP ALA SEQRES 4 B 122 THR ASP ARG CYS CYS PHE VAL HIS ASP CYS CYS TYR GLY SEQRES 5 B 122 LYS LEU THR ASN CYS LYS PRO LYS THR ASP ARG TYR SER SEQRES 6 B 122 TYR SER ARG GLU ASN GLY VAL ILE ILE CYS GLY GLU GLY SEQRES 7 B 122 THR PRO CYS GLU LYS GLN ILE CYS GLU CYS ASP LYS ALA SEQRES 8 B 122 ALA ALA VAL CYS PHE ARG GLU ASN LEU ARG THR TYR LYS SEQRES 9 B 122 LYS ARG TYR MET ALA TYR PRO ASP VAL LEU CYS LYS LYS SEQRES 10 B 122 PRO ALA GLU LYS CYS HET CA A 134 1 HET CA A 135 1 HET CA B 134 1 HET CA B 135 1 HETNAM CA CALCIUM ION FORMUL 3 CA 4(CA 2+) FORMUL 7 HOH *88(H2 O) HELIX 1 1 ASP A 1 GLY A 14 1 14 HELIX 2 2 LEU A 17 TYR A 22 1 6 HELIX 3 3 ASP A 39 LYS A 54 1 16 HELIX 4 4 THR A 88 ASN A 109 1 21 HELIX 5 5 LEU A 110 TYR A 113 5 4 HELIX 6 6 LYS A 114 MET A 118 5 5 HELIX 7 7 PRO A 121 CYS A 126 5 5 HELIX 8 8 ASP B 1 GLY B 14 1 14 HELIX 9 9 ASP B 39 LYS B 54 1 16 HELIX 10 10 THR B 88 ASN B 109 1 21 HELIX 11 11 LEU B 110 TYR B 113 5 4 HELIX 12 12 LYS B 114 MET B 118 5 5 HELIX 13 13 PRO B 121 CYS B 126 5 5 SHEET 1 A 2 TYR A 75 SER A 76 0 SHEET 2 A 2 ILE A 83 CYS A 84 -1 O ILE A 83 N SER A 76 SHEET 1 B 2 TYR B 75 SER B 76 0 SHEET 2 B 2 ILE B 83 CYS B 84 -1 O ILE B 83 N SER B 76 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.05 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.02 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.07 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.02 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.12 SSBOND 8 CYS B 27 CYS B 126 1555 1555 2.04 SSBOND 9 CYS B 29 CYS B 45 1555 1555 2.01 SSBOND 10 CYS B 44 CYS B 105 1555 1555 2.02 SSBOND 11 CYS B 50 CYS B 133 1555 1555 2.00 SSBOND 12 CYS B 51 CYS B 98 1555 1555 2.06 SSBOND 13 CYS B 61 CYS B 91 1555 1555 2.04 SSBOND 14 CYS B 84 CYS B 96 1555 1555 2.06 LINK OH TYR A 22 CA CA A 134 1555 1555 2.67 LINK OD2 ASP A 39 CA CA A 135 1555 1555 2.60 LINK OG1 THR A 41 CA CA A 134 1555 1555 3.18 LINK OG1 THR A 41 CA CA A 135 1555 1555 2.44 LINK O PHE A 106 CA CA A 134 1555 1555 2.85 LINK OG1 THR A 112 CA CA A 135 1555 1555 2.96 LINK OH TYR B 22 CA CA B 134 1555 1555 2.88 LINK OD2 ASP B 39 CA CA B 135 1555 1555 2.79 LINK OG1 THR B 41 CA CA B 134 1555 1555 2.88 LINK OG1 THR B 41 CA CA B 135 1555 1555 2.92 LINK O PHE B 106 CA CA B 134 1555 1555 2.80 LINK OG1 THR B 112 CA CA B 135 1555 1555 2.84 CISPEP 1 PHE A 19 PRO A 20 0 -3.08 CISPEP 2 PHE B 19 PRO B 20 0 -8.44 CISPEP 3 LYS B 128 PRO B 129 0 -0.60 SITE 1 AC1 5 TYR B 22 THR B 41 PHE B 106 ASN B 109 SITE 2 AC1 5 LEU B 110 SITE 1 AC2 4 ASP B 39 ALA B 40 THR B 41 THR B 112 SITE 1 AC3 5 TYR A 22 THR A 41 PHE A 106 LEU A 110 SITE 2 AC3 5 TYR A 113 SITE 1 AC4 4 ASP A 39 THR A 41 ASN A 109 THR A 112 CRYST1 59.236 100.879 47.166 90.00 126.00 90.00 C 1 2 1 8 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 0.016882 0.000000 0.012265 0.00000 SCALE2 0.000000 0.009913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026207 0.00000