HEADER HYDROLASE 16-APR-99 1GOD TITLE MONOMERIC LYS-49 PHOSPHOLIPASE A2 HOMOLOGUE ISOLATED FROM THE VENOM OF TITLE 2 CERROPHIDION (BOTHROPS) GODMANI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PHOSPHOLIPASE A2); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GODMT-II; COMPND 5 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CERROPHIDION GODMANI; SOURCE 3 ORGANISM_TAXID: 44722 KEYWDS LYS49-PHOSPHOLIPASE A2, SNAKE VENOM, BOTHROPS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.ARNI,M.R.M.FONTES,C.BARBERATO,J.M.GUTIERREZ,C.DIAZ-OREIRO, AUTHOR 2 R.J.WARD REVDAT 6 02-AUG-23 1GOD 1 REMARK REVDAT 5 24-FEB-09 1GOD 1 VERSN REVDAT 4 01-APR-03 1GOD 1 JRNL REVDAT 3 24-APR-00 1GOD 1 DBREF REVDAT 2 22-DEC-99 1GOD 1 JRNL HEADER REVDAT 1 23-APR-99 1GOD 0 JRNL AUTH R.K.ARNI,M.R.FONTES,C.BARBERATO,J.M.GUTIERREZ,C.DIAZ, JRNL AUTH 2 R.J.WARD JRNL TITL CRYSTAL STRUCTURE OF MYOTOXIN II, A MONOMERIC JRNL TITL 2 LYS49-PHOSPHOLIPASE A2 HOMOLOGUE ISOLATED FROM THE VENOM OF JRNL TITL 3 CERROPHIDION (BOTHROPS) GODMANI. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 366 177 1999 JRNL REFN ISSN 0003-9861 JRNL PMID 10356281 JRNL DOI 10.1006/ABBI.1999.1210 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.F.DE AZEVEDO JR.,R.J.WARD,J.M.GUTIERREZ,C.DIAZ-OREIRO, REMARK 1 AUTH 2 R.K.ARNI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF A LYS49-PLA2 HOMOLOGUE FROM CERROPHIDION GODMANI VENOM REMARK 1 REF PROTEIN PEPT.LETT. V. 5 121 1998 REMARK 1 REFN ISSN 0929-8665 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.1 REMARK 3 NUMBER OF REFLECTIONS : 3129 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) : 0.188 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 327 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 50.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 288 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 37 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.068 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 949 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.53 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.220 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000000862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-95 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.6 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22540 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1CLP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE (PH 4.6), 2.0 M REMARK 280 (NH4)2SO4, 1MM NANO3, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 42.36000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.28000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.54000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.28000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.18000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.28000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.54000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.28000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.18000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 42.36000 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: MONOMERIC 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 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 A 138 O HOH A 139 3554 1.99 REMARK 500 OD2 ASP A 131 O HOH A 139 3554 2.06 REMARK 500 O HOH A 162 O HOH A 163 6565 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 ALA A 18 -79.98 -44.13 REMARK 500 ARG A 34 146.83 -171.46 REMARK 500 ASP A 39 179.38 179.40 REMARK 500 ASP A 79 81.02 46.88 REMARK 500 CYS A 84 -103.69 -63.20 REMARK 500 ASP A 86 -163.42 -160.83 REMARK 500 ASN A 88 171.49 69.34 REMARK 500 ASP A 111 14.24 -62.63 REMARK 500 PRO A 121 -99.26 -40.06 REMARK 500 LYS A 122 -55.56 168.42 REMARK 500 CYS A 126 -167.54 -103.82 REMARK 500 REMARK 500 REMARK: NULL DBREF 1GOD A 1 121 UNP P81165 PA22_CERGO 1 121 SEQRES 1 A 121 SER MET TYR GLN LEU TRP LYS MET ILE LEU GLN GLU THR SEQRES 2 A 121 GLY LYS ASN ALA VAL PRO SER TYR GLY LEU TYR GLY CYS SEQRES 3 A 121 ASN CYS GLY VAL GLY SER ARG GLY LYS PRO LYS ASP ALA SEQRES 4 A 121 THR ASP ARG CYS CYS PHE VAL HIS LYS CYS CYS TYR LYS SEQRES 5 A 121 LYS LEU THR ASP CYS SER PRO LYS THR ASP SER TYR SER SEQRES 6 A 121 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY ASP ASN SEQRES 7 A 121 ASN PRO CYS LEU GLN GLU MET CYS GLU CYS ASP LYS ALA SEQRES 8 A 121 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 A 121 LYS ASN TYR LYS ILE TYR PRO LYS PRO LEU CYS LYS LYS SEQRES 10 A 121 ALA ASP ALA CYS FORMUL 2 HOH *50(H2 O) HELIX 1 1 MET A 2 THR A 13 1 12 HELIX 2 2 ALA A 18 SER A 21 1 4 HELIX 3 3 ALA A 40 LYS A 57 1 15 HELIX 4 4 CYS A 90 GLU A 108 1 18 HELIX 5 5 LEU A 110 THR A 112 5 3 SHEET 1 A 2 SER A 76 TRP A 77 0 SHEET 2 A 2 ILE A 82 VAL A 83 -1 N VAL A 83 O SER A 76 SSBOND 1 CYS A 27 CYS A 126 1555 1555 2.03 SSBOND 2 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 3 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 4 CYS A 50 CYS A 133 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 90 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.02 CRYST1 60.560 60.560 84.720 90.00 90.00 90.00 P 43 21 2 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 0.016512 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011803 0.00000