HEADER HYDROLASE 19-AUG-02 1MH8 TITLE CRYSTAL STRUCTURE OF A PHOPHOLIPASE A2 MONOMER WITH ISOLEUCINE AT TITLE 2 SECOND POSITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA SAGITTIFERA; SOURCE 3 ORGANISM_TAXID: 195058; SOURCE 4 SECRETION: VENOM KEYWDS PHOSPHOLIPASE, ENZYME, PHOSPHOLIPIDS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.JABEEN,J.JASTI,N.SINGH,R.K.SINGH,S.SHARMA,T.P.SINGH REVDAT 3 30-OCT-24 1MH8 1 REMARK REVDAT 2 24-FEB-09 1MH8 1 VERSN REVDAT 1 10-JUN-03 1MH8 0 JRNL AUTH T.JABEEN,J.JASTI,N.SINGH,R.K.SINGH,S.SHARMA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF A PHOSPHOLIPASE A2 MONOMER WITH JRNL TITL 2 ISOLEUCINE AT SECOND POSITION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 9477 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) : 0.197 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 506 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1283 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 73 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 923 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.20 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.24 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) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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) : 1.430 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.220 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.510 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.790 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 52.75 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 298 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 RU200 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9835 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 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: 1LFJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM SODIUM PHOSPHATE, 2MM CACL2, 25% REMARK 280 ETHANOL, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 32.99700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 16.49850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.49550 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 ASP A 24 75.83 -153.89 REMARK 500 ASP A 39 -168.84 -163.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LFJ RELATED DB: PDB REMARK 900 1LFJ IS THE X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN TWO REMARK 900 HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA: REMARK 900 PRINCIPLE OF MOLECULAR ASSOCIATION AND INACTIVATION REMARK 900 RELATED ID: 1LFF RELATED DB: PDB REMARK 900 1LFF IS THE CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM REMARK 900 NAJA NAJA SAGITTIFERA AT 1.5 RESOLUTION REMARK 900 RELATED ID: 1LN8 RELATED DB: PDB REMARK 900 1LN8 IS THE CRYSTAL STRUCTURE OF A NEW ISOFORM OF PHOSPHOLIPASE A2 REMARK 900 FROM NAJA NAJA SAGITTIFERA AT 1.6 RESOLUTION REMARK 900 RELATED ID: 1MF4 RELATED DB: PDB REMARK 900 1MF4 IS THE STRUCTURE-BASED DESIGN OF POTENT AND SELECTIVE REMARK 900 INHIBITORS OF PHOSPHOLIPASE A2: CRYSTAL STRUCTURE OF THE COMPLEX REMARK 900 FORMED BETWEEN PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AND A REMARK 900 DESIGNED PEPTIDE INHIBITOR AT 1.9 RESOLUTION DBREF 1MH8 A 1 120 UNP P60043 PA21B_NAJSG 8 126 SEQRES 1 A 119 ASN ILE TYR GLN PHE LYS ASN MET ILE GLU CYS THR VAL SEQRES 2 A 119 PRO ALA ARG SER TRP TRP ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY GLY GLY GLY SER GLY THR PRO THR ASP ASP SEQRES 4 A 119 LEU ASP ARG CYS CYS GLN VAL HIS ASP ASN CYS TYR ASN SEQRES 5 A 119 GLN ALA GLN GLU ILE THR GLY CYS ARG PRO LYS TRP LYS SEQRES 6 A 119 THR TYR THR TYR GLN CYS THR GLN GLY THR LEU THR CYS SEQRES 7 A 119 LYS GLY ARG ASN ASN ALA CYS ALA ALA THR THR CYS ASP SEQRES 8 A 119 CYS ASP ARG LEU ALA ALA ILE CYS PHE ALA GLY ALA PRO SEQRES 9 A 119 TYR ASN ASP THR ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS GLN FORMUL 2 HOH *84(H2 O) HELIX 1 1 ASN A 1 VAL A 13 1 13 HELIX 2 2 SER A 18 PHE A 22 5 5 HELIX 3 3 ASP A 39 GLN A 56 1 18 HELIX 4 4 ASN A 84 ALA A 104 1 21 HELIX 5 5 ASN A 107 TYR A 111 5 5 HELIX 6 6 ASP A 114 CYS A 119 1 6 SHEET 1 A 2 ASP A 24 TYR A 25 0 SHEET 2 A 2 CYS A 29 GLY A 30 -1 O CYS A 29 N TYR A 25 SHEET 1 B 2 TYR A 70 THR A 73 0 SHEET 2 B 2 THR A 76 CYS A 79 -1 O THR A 78 N GLN A 71 SSBOND 1 CYS A 11 CYS A 72 1555 1555 2.02 SSBOND 2 CYS A 27 CYS A 119 1555 1555 2.03 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 4 CYS A 44 CYS A 100 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 93 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 86 1555 1555 2.03 SSBOND 7 CYS A 79 CYS A 91 1555 1555 2.03 CRYST1 42.817 42.817 65.994 90.00 90.00 90.00 P 41 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 0.023355 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015153 0.00000