HEADER HYDROLASE 02-JUL-07 2QHE TITLE CRYSTAL STRUCTURE OF SER49-PLA2 (ECARPHOLIN S) FROM ECHIS CARINATUS TITLE 2 SOCHUREKI SNAKE VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ECARPHOLIN S, PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE; COMPND 5 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ECHIS CARINATUS; SOURCE 3 ORGANISM_COMMON: SAW-SCALED VIPER; SOURCE 4 ORGANISM_TAXID: 40353; SOURCE 5 OTHER_DETAILS: SNAKE VENOM GLAND KEYWDS BETA SHEET, THREE HELICES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHOU,S.VALIYAVEETTIL,M.L.GO,R.M.KINI,J.SIVARAMAN REVDAT 5 25-OCT-23 2QHE 1 REMARK REVDAT 4 18-OCT-17 2QHE 1 REMARK REVDAT 3 24-FEB-09 2QHE 1 VERSN REVDAT 2 30-SEP-08 2QHE 1 JRNL REVDAT 1 16-OCT-07 2QHE 0 JRNL AUTH X.ZHOU,T.C.TAN,S.VALIYAVEETTIL,M.L.GO,R.M.KINI, JRNL AUTH 2 A.VELAZQUEZ-CAMPOY,J.SIVARAMAN JRNL TITL STRUCTURAL CHARACTERIZATION OF MYOTOXIC ECARPHOLIN S FROM JRNL TITL 2 ECHIS CARINATUS VENOM JRNL REF BIOPHYS.J. V. 95 3366 2008 JRNL REFN ISSN 0006-3495 JRNL PMID 18586854 JRNL DOI 10.1529/BIOPHYSJ.107.117747 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 110.00 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 6322 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 611 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 441 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 18 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 959 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03800 REMARK 3 B22 (A**2) : -0.10800 REMARK 3 B33 (A**2) : 0.06900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.258 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.199 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.715 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.944 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.724 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 92.95 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2QHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000043601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6463 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.8000 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 (%) : 87.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 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, MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1JIA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 26.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 20% ISO-PROPANOL, 0.1M REMARK 280 SODIUM CITRATE PH5.6, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.11550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.47100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.74350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.47100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.11550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.74350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 SER A 24 17.32 -142.02 REMARK 500 ASP A 39 -170.00 -164.20 REMARK 500 SER A 90 -79.80 -35.67 REMARK 500 LYS A 132 -53.43 71.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QHD RELATED DB: PDB REMARK 900 RELATED ID: 2QHG RELATED DB: PDB DBREF 2QHE A 1 133 UNP P48650 PA2N_ECHCA 1 122 SEQRES 1 A 122 SER VAL VAL GLU LEU GLY LYS MET ILE ILE GLN GLU THR SEQRES 2 A 122 GLY LYS SER PRO PHE PRO SER TYR THR SER TYR GLY CYS SEQRES 3 A 122 PHE CYS GLY GLY GLY GLU ARG GLY PRO PRO LEU ASP ALA SEQRES 4 A 122 THR ASP ARG CYS CYS LEU ALA HIS SER CYS CYS TYR ASP SEQRES 5 A 122 THR LEU PRO ASP CYS SER PRO LYS THR ASP ARG TYR LYS SEQRES 6 A 122 TYR LYS ARG GLU ASN GLY GLU ILE ILE CYS GLU ASN SER SEQRES 7 A 122 THR SER CYS LYS LYS ARG ILE CYS GLU CYS ASP LYS ALA SEQRES 8 A 122 VAL ALA VAL CYS LEU ARG LYS ASN LEU ASN THR TYR ASN SEQRES 9 A 122 LYS LYS TYR THR TYR TYR PRO ASN PHE TRP CYS LYS GLY SEQRES 10 A 122 ASP ILE GLU LYS CYS FORMUL 2 HOH *96(H2 O) HELIX 1 1 SER A 1 GLY A 14 1 14 HELIX 2 2 SER A 17 TYR A 22 1 6 HELIX 3 3 ASP A 39 ASP A 53 1 15 HELIX 4 4 THR A 89 ASN A 109 1 21 HELIX 5 5 LEU A 110 TYR A 113 5 4 HELIX 6 6 ASN A 114 THR A 118 5 5 HELIX 7 7 PRO A 121 CYS A 126 5 5 SHEET 1 A 2 TYR A 75 GLU A 78 0 SHEET 2 A 2 GLU A 81 CYS A 84 -1 O ILE A 83 N LYS 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 2.04 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.03 CISPEP 1 PHE A 19 PRO A 20 0 1.23 CISPEP 2 GLY A 35 PRO A 36 0 -0.80 CRYST1 34.231 39.487 68.942 90.00 90.00 90.00 P 21 21 21 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 0.029213 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014505 0.00000