HEADER HYDROLASE 05-APR-04 1SZ8 TITLE CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA NAJA TITLE 2 SAGITTIFERA AT 1.5 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2 ISOFORM 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE; COMPND 5 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 A2, MOLECULAR CONFORMATION, ENZYME ACTIVITY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SINGH,S.SHARMA,T.JABEEN,P.KAUR,T.P.SINGH REVDAT 5 25-OCT-23 1SZ8 1 REMARK LINK REVDAT 4 07-FEB-18 1SZ8 1 REMARK REVDAT 3 16-APR-14 1SZ8 1 REMARK VERSN REVDAT 2 24-FEB-09 1SZ8 1 VERSN REVDAT 1 20-APR-04 1SZ8 0 SPRSDE 20-APR-04 1SZ8 1LFF JRNL AUTH R.K.SINGH,S.SHARMA,T.JABEEN,P.KAUR,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA JRNL TITL 2 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 BETWEEN TWO REMARK 1 TITL 2 HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM NAJA NAJA REMARK 1 TITL 3 SAGITTIFERA: PRINCIPLE OF MOLECULAR ASSOCIATION AND REMARK 1 TITL 4 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,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.233 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 : 913 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 143 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.93 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 1SZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022115. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-01 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 : 13.60 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 (%): 44.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, CACL2, PH 6.00, REMARK 280 VAPOR DIFFUSION, HANGING 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 32.22550 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 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 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 15 C ARG A 17 N 0.290 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 15 O - C - N ANGL. DEV. = -10.2 DEGREES REMARK 500 LYS A 31 CG - CD - CE ANGL. DEV. = 21.0 DEGREES REMARK 500 THR A 36 CB - CA - C ANGL. DEV. = -19.3 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 ASP A 24 81.15 -154.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 28 O REMARK 620 2 GLY A 30 O 95.0 REMARK 620 3 GLY A 32 O 74.1 86.8 REMARK 620 4 ASP A 49 OD1 79.7 145.1 123.7 REMARK 620 5 ASP A 49 OD2 63.5 156.1 77.7 46.0 REMARK 620 6 ACY A 401 O 80.2 77.3 148.4 67.8 107.0 REMARK 620 7 HOH A 526 O 150.4 83.8 76.3 117.3 109.5 127.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 401 DBREF 1SZ8 A 1 120 UNP P60045 PA23_NAJSG 8 126 SEQRES 1 A 119 ASN LEU TYR GLN PHE LYS ASN MET ILE GLN CYS THR VAL SEQRES 2 A 119 PRO SER ARG SER TRP GLN ASP PHE ALA ASP TYR GLY CYS SEQRES 3 A 119 TYR CYS GLY LYS GLY GLY SER GLY THR PRO VAL ASP ASP 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 THR 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 ASP ALA ASN TYR ASN ILE ASP LEU LYS ALA ARG SEQRES 10 A 119 CYS ASN HET CA A 201 1 HET PO4 A 301 5 HET ACY A 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 *143(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 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 THR 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 1555 1555 2.01 SSBOND 2 CYS A 27 CYS A 119 1555 1555 2.03 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.04 SSBOND 4 CYS A 44 CYS A 100 1555 1555 2.01 SSBOND 5 CYS A 51 CYS A 93 1555 1555 2.01 SSBOND 6 CYS A 61 CYS A 86 1555 1555 2.04 SSBOND 7 CYS A 79 CYS A 91 1555 1555 2.04 LINK O TYR A 28 CA CA A 201 1555 1555 2.64 LINK O GLY A 30 CA CA A 201 1555 1555 2.35 LINK O GLY A 32 CA CA A 201 1555 1555 2.58 LINK OD1 ASP A 49 CA CA A 201 1555 1555 2.73 LINK OD2 ASP A 49 CA CA A 201 1555 1555 2.74 LINK CA CA A 201 O ACY A 401 1555 1555 2.75 LINK CA CA A 201 O HOH A 526 1555 1555 2.63 SITE 1 AC1 6 TYR A 28 GLY A 30 GLY A 32 ASP A 49 SITE 2 AC1 6 ACY A 401 HOH A 526 SITE 1 AC2 9 GLU A 54 ASN A 57 ARG A 62 LYS A 66 SITE 2 AC2 9 THR A 67 GLN A 74 HOH A 422 HOH A 503 SITE 3 AC2 9 HOH A 504 SITE 1 AC3 7 TYR A 28 GLY A 30 HIS A 48 ASP A 49 SITE 2 AC3 7 CA A 201 HOH A 481 HOH A 525 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