HEADER HYDROLASE 11-APR-02 1LFF OBSLTE 20-APR-04 1LFF 1SZ8 TITLE CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA TITLE 2 NAJA SAGITTIFERA AT 1.5 A 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 NAJA SAGITTIFERA; SOURCE 3 ORGANISM_COMMON: INDIAN COBRA; SOURCE 4 SECRETION: VENOM KEYWDS PHOSPHOLIPASE A2, MOLECULAR CONFORMATION, ENZYME ACTIVITY EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SINGH,S.SHARMA,T.JABEEN,P.KAUR,T.P.SINGH REVDAT 2 20-APR-04 1LFF 1 OBSLTE REVDAT 1 20-MAY-03 1LFF 0 JRNL AUTH R.K.SINGH,S.SHARMA,T.JABEEN,P.KAUR,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 JRNL TITL 2 FROM NAJA NAJA SAGITTIFERA AT 1.5 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.JABEEN,S.SHARMA,R.K.SINGH,P.KAUR,T.P.SINGH REMARK 1 TITL X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED REMARK 1 TITL 2 BETWEEN TWO HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE REMARK 1 TITL 3 A2 FROM NAJA NAJA SAGITTIFERA: PRINCIPLE OF REMARK 1 TITL 4 MOLECULAR ASSOCIATION AND INACTIVATION REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 1.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 17006 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 565 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 908 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.40 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) : 0.009 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.025 ; 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 1LFF COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-2002. REMARK 100 THE RCSB ID CODE IS RCSB015898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-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 : MIRROR 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 : 17571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 13.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03800 REMARK 200 FOR THE DATA SET : 26.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.37000 REMARK 200 FOR SHELL : 3.000 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 (%): 44.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 32.22550 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 16.11275 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 48.33825 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 1 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 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 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 GLN A 4 CB GLN A 4 CG -0.107 REMARK 500 GLN A 4 CG GLN A 4 CD -0.105 REMARK 500 GLN A 4 CD GLN A 4 OE1 0.128 REMARK 500 GLN A 4 CA GLN A 4 C -0.087 REMARK 500 SER A 15 CA SER A 15 C 0.112 REMARK 500 ARG A 17 N ARG A 17 CA 0.132 REMARK 500 SER A 15 C ARG A 17 N 0.126 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 GLN A 4 OE1 - CD - NE2 ANGL. DEV. =-21.8 DEGREES REMARK 500 GLN A 4 CG - CD - NE2 ANGL. DEV. = 13.6 DEGREES REMARK 500 THR A 36 CB - CA - C ANGL. DEV. =-17.4 DEGREES SEQRES 1 A 119 ASN LEU TYR GLN PHE LYS ASN MET ILE ASP CYS THR VAL SEQRES 2 A 119 PRO SER ARG SER TRP GLU ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY GLY GLY GLY SER GLY THR PRO VAL ASP LYS SEQRES 4 A 119 LEU ASP ARG CYS CYS GLN VAL HIS ASP ASN CYS TYR ASN SEQRES 5 A 119 GLU ALA GLU ASN ILE SER GLY CYS ARG PRO TYR PHE LYS SEQRES 6 A 119 THR TYR SER TYR GLU CYS SER GLN GLY THR LEU THR CYS SEQRES 7 A 119 LYS GLY ASP ASN ASN ALA CYS ALA ALA SER VAL 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 LEU ALA ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS LYS HET CA A 201 1 HET PO4 301 5 HET ACY 401 4 HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION HETNAM ACY ACETIC ACID FORMUL 2 CA CA 2+ FORMUL 3 PO4 O4 P 3- FORMUL 4 ACY C2 H4 O2 FORMUL 5 HOH *146(H2 O1) 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 GLU 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 SER A 73 0 SHEET 2 B 2 THR A 76 CYS A 79 -1 O THR A 78 N GLU A 71 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 CRYST1 42.017 42.017 64.451 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 0.023800 -0.000001 -0.000001 0.00000 SCALE2 0.000000 0.023800 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.015516 0.00000