HEADER HYDROLASE 11-APR-02 1LFJ OBSLTE 10-FEB-04 1LFJ 1S6B TITLE X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN TWO TITLE 2 HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM NAJA NAJA TITLE 3 SAGITTIFERA: PRINCIPLE OF MOLECULAR ASSOCIATION AND TITLE 4 INACTIVATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PHOSPHOLIPASE A2; COMPND 7 CHAIN: B; COMPND 8 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA NAJA SAGITTIFERA; SOURCE 3 ORGANISM_COMMON: INDIAN COBRA; SOURCE 4 SECRETION: VENOM; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: NAJA NAJA SAGITTIFERA; SOURCE 7 ORGANISM_COMMON: INDIAN COBRA; SOURCE 8 SECRETION: VENOM KEYWDS PHOSPHOLIPASE A2, MOLECULAR CONFORMATION, ENZYME ACTIVITY EXPDTA X-RAY DIFFRACTION AUTHOR T.JABEEN,S.SHARMA,R.K.SINGH,P.KAUR,T.P.SINGH REVDAT 2 10-FEB-04 1LFJ 1 OBSLTE REVDAT 1 20-MAY-03 1LFJ 0 JRNL AUTH T.JABEEN,S.SHARMA,R.K.SINGH,P.KAUR,T.P.SINGH JRNL TITL X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED JRNL TITL 2 BETWEEN TWO HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE JRNL TITL 3 A2 FROM NAJA NAJA SAGITTIFERA: PRINCIPLE OF JRNL TITL 4 MOLECULAR ASSOCIATION AND INACTIVATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.K.SINGH,S.SHARMA,T.JABEEN,P.KAUR,T.P.SINGH REMARK 1 TITL CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 REMARK 1 TITL 2 FROM NAJA NAJA SAGITTIFERA AT 1.5 A RESOLUTION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 27946 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.025 REMARK 3 FREE R VALUE TEST SET COUNT : 730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1819 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 363 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.80 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.033 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL 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 OTHER REFINEMENT REMARKS: USED CONJUGATE DIRECTION METHOD REMARK 4 REMARK 4 1LFJ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-2002. REMARK 100 THE RCSB ID CODE IS RCSB015899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-2001 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.80200 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD 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 : 27946 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : 17.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32900 REMARK 200 FOR SHELL : 3.020 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 1PSH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM PHOSPHATE, CALCIUM CHLORIDE, REMARK 280 ETHANOL, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K 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,1/2+Z REMARK 290 3555 -Y,X,1/4+Z REMARK 290 4555 Y,-X,3/4+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 28.55750 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 14.27875 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 42.83625 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O GLY A 76 O HOH 143 2.10 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 2 CB THR A 2 OG1 0.089 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 73 CD - CE - NZ ANGL. DEV. = 31.5 DEGREES REMARK 500 ARG A 118 CD - NE - CZ ANGL. DEV. = 19.1 DEGREES REMARK 500 ARG B 2 CD - NE - CZ ANGL. DEV. = 20.3 DEGREES REMARK 500 ASP B 49 N - CA - CB ANGL. DEV. = 20.4 DEGREES REMARK 500 ARG B 118 CD - NE - CZ ANGL. DEV. = 20.5 DEGREES REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 307 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH 326 DISTANCE = 6.61 ANGSTROMS SEQRES 1 A 119 ASN THR TYR GLN PHE GLN ASN MET ILE GLN CYS THR VAL SEQRES 2 A 119 PRO LYS ARG SER TRP ARG ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY ARG GLY GLY SER GLY THR PRO ILE ASP ASP SEQRES 4 A 119 LEU ASP SER CYS CYS GLN VAL HIS ASP ASN CYS TYR ASN SEQRES 5 A 119 SER ALA ARG GLU GLN GLY GLY CYS ARG PRO LYS GLN LYS SEQRES 6 A 119 THR TYR THR TYR GLN CYS LYS ALA GLY GLY LEU SER CYS SEQRES 7 A 119 SER GLY ALA 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 ASN ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS GLN SEQRES 1 B 119 ASN ARG TRP GLN PHE LYS ASN MET ILE SER CYS THR VAL SEQRES 2 B 119 PRO SER ARG SER TRP TRP ASP PHE ALA ASP TYR GLY CYS SEQRES 3 B 119 TYR CYS GLY ARG GLY GLY SER GLY THR PRO SER ASP ASP SEQRES 4 B 119 LEU ASP ARG CYS CYS GLN THR HIS ASP ASN CYS TYR ASN SEQRES 5 B 119 GLU ALA GLU LYS ILE SER GLY CYS ASN PRO ARG PHE ARG SEQRES 6 B 119 THR TYR SER TYR ALA CYS THR ALA GLY THR LEU THR CYS SEQRES 7 B 119 THR GLY ARG ASN ASN ALA CYS ALA ALA SER VAL CYS ASP SEQRES 8 B 119 CYS ASP ARG ASN ALA ALA ILE CYS PHE ALA GLY ALA PRO SEQRES 9 B 119 TYR ASN ASP SER ASN TYR ASN ILE ASP LEU GLN ALA ARG SEQRES 10 B 119 CYS ASN HET CA 401 1 HET CA B 402 1 HET PO4 501 5 HET PO4 502 5 HET ACY 601 4 HET ACY 602 4 HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION HETNAM ACY ACETIC ACID FORMUL 3 CA 2(CA 2+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 ACY 2(C2 H4 O2) FORMUL 9 HOH *355(H2 O1) HELIX 1 1 ASN A 1 VAL A 13 1 13 HELIX 2 2 TRP A 19 ASP A 24 1 6 HELIX 3 3 ASP A 39 ARG 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 HELIX 7 7 ASN B 1 VAL B 13 1 13 HELIX 8 8 SER B 18 ALA B 23 5 6 HELIX 9 9 ASP B 39 GLU B 56 1 18 HELIX 10 10 ASN B 84 ALA B 104 1 21 HELIX 11 11 ASN B 107 TYR B 111 5 5 HELIX 12 12 ASP B 114 CYS B 119 1 6 SHEET 1 A 2 TYR A 70 LYS A 73 0 SHEET 2 A 2 GLY A 76 CYS A 79 -1 O GLY A 76 N LYS A 73 SHEET 1 B 2 TYR B 70 THR B 73 0 SHEET 2 B 2 THR B 76 CYS B 79 -1 O THR B 76 N THR B 73 SSBOND 1 CYS A 11 CYS A 72 SSBOND 2 CYS A 27 CYS A 119 SSBOND 3 CYS A 29 CYS A 45 SSBOND 4 CYS A 44 CYS A 100 SSBOND 5 CYS A 51 CYS A 93 SSBOND 6 CYS A 61 CYS A 86 SSBOND 7 CYS A 79 CYS A 91 SSBOND 8 CYS B 11 CYS B 72 SSBOND 9 CYS B 27 CYS B 119 SSBOND 10 CYS B 29 CYS B 45 SSBOND 11 CYS B 44 CYS B 100 SSBOND 12 CYS B 51 CYS B 93 SSBOND 13 CYS B 61 CYS B 86 SSBOND 14 CYS B 79 CYS B 91 CRYST1 64.537 64.537 57.115 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 0.015495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017509 0.00000