10 20 30 40 50 60 70 80 1MH7 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 19-AUG-02 1MH7
TITLE CRYSTAL STRUCTURE OF A CALCIUM-FREE ISOFORM OF TITLE 2 PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 2.0 A TITLE 3 RESOLUTION
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,R.K.SINGH,S.SUJATA,T.P.SINGH
REVDAT 2 24-FEB-09 1MH7 1 VERSN REVDAT 1 20-MAY-03 1MH7 0
JRNL AUTH T.JABEEN,J.JASTI,R.K.SINGH,S.SUJATA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF A CALCIUM-FREE ISOFORM OF JRNL TITL 2 PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 2.0 JRNL TITL 3 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 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) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 7594 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) : 0.199 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 399 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 932 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE : 0.2320 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 50 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.033 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 924 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.20 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.60 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.49 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) : 1.570 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.430 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.800 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.190 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 34.06 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 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1MH7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-02. REMARK 100 THE RCSB ID CODE IS RCSB016909.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-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 : GRAPHITE REMARK 200 OPTICS : MONOCHRMOATOR 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 : 7717 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.1000 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 (%) : 82.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : 0.23700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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 (%): 45.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM SODIUM PHOSPHATE, 2MM CACL2, REMARK 280 28% ETHANOL, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 32.88850 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 16.44425 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 49.33275 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 2 N - CA - CB ANGL. DEV. = -13.4 DEGREES REMARK 500 LEU A 2 CA - CB - CG ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 82 CB - CA - C ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 THR A 90 CA - CB - OG1 ANGL. DEV. = 15.2 DEGREES REMARK 500 THR A 90 CA - CB - CG2 ANGL. DEV. = 10.1 DEGREES 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 15 36.57 -80.69 REMARK 500 ARG A 17 149.44 -170.40 REMARK 500 ASP A 24 75.61 -154.96 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 REMARK 900 BETWEEN TWO HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM REMARK 900 NAJA NAJA SAGITTIFERA: PRINCIPLE OF MOLECULAR ASSOCIATION REMARK 900 AND INACTIVATION REMARK 900 RELATED ID: 1LFF RELATED DB: PDB REMARK 900 1LFF IS THE CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 REMARK 900 FROM NAJA NAJA SAGITTIFERA AT 1.5 A RESOLUTION REMARK 900 RELATED ID: 1LN8 RELATED DB: PDB REMARK 900 1LN8 IS THE CRYSTAL STRUCTURE OF A NEW ISOFORM OF REMARK 900 PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 1.6 A REMARK 900 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 REMARK 900 COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 FROM NAJA NAJA REMARK 900 SAGITTIFERA AND A DESIGNED PEPTIDE INHIBITOR AT 1.9 A REMARK 900 RESOLUTION
DBREF 1MH7 A 1 120 UNP P60043 PA21B_NAJSG 8 126
SEQRES 1 A 119 ASN LEU 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 SER 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 *74(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 2.00 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 2.02 SSBOND 7 CYS A 79 CYS A 91 1555 1555 2.03
CRYST1 42.758 42.758 65.777 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 0.023387 0.000000 0.000000 0.00000
SCALE2 0.000000 0.023387 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015203 0.00000