HEADER TOXIN 21-JUL-00 1FE5 TITLE SEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM COMMON TITLE 2 KRAIT (BUNGARUS CAERULEUS) AT 2.4 RESOLUTION: IDENTIFICATION AND TITLE 3 CHARACTERIZATION OF ITS PHARMACOLOGICAL SITES. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NATURAL PROTEIN; COMPND 5 EC: 3.1.1.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BUNGARUS CAERULEUS; SOURCE 3 ORGANISM_TAXID: 132961; SOURCE 4 SECRETION: VENOM KEYWDS BUNGARUS CAERULEUS; PHOSPHOLIPASE A2 (PLA2); PRESYNAPTIC NEUROTOXIN; KEYWDS 2 NEUROTOXIC SITE; X-RAY STRUCTURE; MOLECULAR REPLACEMENT, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR G.SINGH,S.GOURINATH,S.SHARMA,M.PARAMASIVAM,A.SRINIVASAN,T.P.SINGH REVDAT 5 13-NOV-24 1FE5 1 REMARK LINK REVDAT 4 04-OCT-17 1FE5 1 REMARK REVDAT 3 24-FEB-09 1FE5 1 VERSN REVDAT 2 18-APR-01 1FE5 1 JRNL REVDAT 1 24-JAN-01 1FE5 0 JRNL AUTH G.SINGH,S.GOURINATH,S.SHARMA,M.PARAMASIVAM,A.SRINIVASAN, JRNL AUTH 2 T.P.SINGH JRNL TITL SEQUENCE AND CRYSTAL STRUCTURE DETERMINATION OF A BASIC JRNL TITL 2 PHOSPHOLIPASE A2 FROM COMMON KRAIT (BUNGARUS CAERULEUS) AT JRNL TITL 3 2.4 A RESOLUTION: IDENTIFICATION AND CHARACTERIZATION OF ITS JRNL TITL 4 PHARMACOLOGICAL SITES. JRNL REF J.MOL.BIOL. V. 307 1049 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11286555 JRNL DOI 10.1006/JMBI.2001.4550 REMARK 2 REMARK 2 RESOLUTION. 2.45 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 151511.230 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 4535 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) : 0.201 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.900 REMARK 3 FREE R VALUE TEST SET COUNT : 356 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.014 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 521 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.051 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 897 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 77 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 3.59000 REMARK 3 B13 (A**2) : 3.59000 REMARK 3 B23 (A**2) : 3.59000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.42 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.840 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) : 1.740 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.740 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.060 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.520 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.41 REMARK 3 BSOL : 71.46 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.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 1FE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011507. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4629 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 17.30 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.22300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, CACL2, DIOXANE, REMARK 280 SODIUM CACODYLATE , PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 Z,X,Y REMARK 290 3555 Y,Z,X REMARK 290 4555 -Y,-X,-Z REMARK 290 5555 -X,-Z,-Y REMARK 290 6555 -Z,-Y,-X 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 -0.035248 -0.036513 0.998711 0.00000 REMARK 290 SMTRY2 2 0.999379 -0.001288 0.035225 0.00000 REMARK 290 SMTRY3 2 0.000000 0.999332 0.036536 0.00000 REMARK 290 SMTRY1 3 -0.035248 0.999379 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.036513 -0.001288 0.999332 0.00000 REMARK 290 SMTRY3 3 0.998711 0.035225 0.036536 0.00000 REMARK 290 SMTRY1 4 0.035248 -0.999379 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.999379 -0.035248 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 0.036536 -0.999332 0.00000 REMARK 290 SMTRY3 5 0.000000 -0.999332 -0.036536 0.00000 REMARK 290 SMTRY1 6 0.035248 0.036513 -0.998711 0.00000 REMARK 290 SMTRY2 6 0.036513 -0.998712 -0.035225 0.00000 REMARK 290 SMTRY3 6 -0.998711 -0.035225 -0.036536 0.00000 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 300 REMARK: PHOSPHOLIPASE A2 MONOMER IN REMARK 300 EACH ASSYMETRIC UNIT 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 234 O HOH A 234 4776 1.85 REMARK 500 O HOH A 244 O HOH A 244 5766 1.97 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 THR A 73 74.89 -115.71 REMARK 500 GLU A 74 128.89 -31.26 REMARK 500 PRO A 75 36.82 -94.50 REMARK 500 THR A 82 -23.25 -146.58 REMARK 500 MET A 112 68.64 62.99 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 150 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 28 O REMARK 620 2 GLY A 30 O 82.5 REMARK 620 3 GLY A 32 O 80.5 70.2 REMARK 620 4 ASP A 49 OD1 100.1 153.1 136.7 REMARK 620 5 ASP A 49 OD2 82.4 158.8 92.7 45.4 REMARK 620 6 HOH A 252 O 173.4 91.7 94.6 86.5 102.4 REMARK 620 N 1 2 3 4 5 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 150 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DPY RELATED DB: PDB REMARK 900 STRUCTURE OF KRAIT PLA2 AT 2.45 RESOLUTION DBREF 1FE5 A 1 120 UNP Q9DF52 PA2K_BUNCE 28 145 SEQRES 1 A 118 ASN LEU ILE GLN PHE LYS ASN MET ILE GLN CYS ALA GLY SEQRES 2 A 118 THR ARG PRO TRP THR ALA TYR VAL ASN TYR GLY CYS TYR SEQRES 3 A 118 CYS GLY LYS GLY GLY SER GLY THR PRO VAL ASP GLU LEU SEQRES 4 A 118 ASP ARG CYS CYS TYR THR HIS ASP ASN CYS TYR ASN GLU SEQRES 5 A 118 ALA GLU LYS ILE PRO GLY CYS ASN PRO ASN ILE LYS THR SEQRES 6 A 118 TYR SER TYR THR CYS THR GLU PRO ASN LEU THR CYS THR SEQRES 7 A 118 ASP THR ALA ASP THR CYS ALA ARG PHE LEU CYS ASN CYS SEQRES 8 A 118 ASP ARG THR ALA ALA ILE CYS PHE ALA SER ALA PRO TYR SEQRES 9 A 118 ASN SER ASN ASN VAL MET ILE SER SER SER THR ASN CYS SEQRES 10 A 118 GLN HET CA A 150 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *77(H2 O) HELIX 1 1 ASN A 1 GLY A 13 1 13 HELIX 2 2 PRO A 18 VAL A 23 5 6 HELIX 3 3 ASP A 39 GLU A 56 1 18 HELIX 4 4 ASP A 84 ALA A 104 1 21 HELIX 5 5 ASN A 107 VAL A 111 5 5 SHEET 1 A 2 TYR A 70 THR A 73 0 SHEET 2 A 2 ASN A 76 CYS A 79 -1 O ASN A 76 N THR A 73 SSBOND 1 CYS A 11 CYS A 72 1555 1555 2.03 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 2.04 SSBOND 7 CYS A 79 CYS A 91 1555 1555 2.02 LINK O TYR A 28 CA CA A 150 1555 1555 2.62 LINK O GLY A 30 CA CA A 150 1555 1555 2.61 LINK O GLY A 32 CA CA A 150 1555 1555 2.80 LINK OD1 ASP A 49 CA CA A 150 1555 1555 2.96 LINK OD2 ASP A 49 CA CA A 150 1555 1555 2.72 LINK CA CA A 150 O HOH A 252 1555 5766 3.33 CISPEP 1 GLU A 74 PRO A 75 0 0.17 SITE 1 AC1 4 TYR A 28 GLY A 30 GLY A 32 ASP A 49 CRYST1 57.980 57.980 57.980 92.02 92.02 92.02 R 3 2 6 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 0.017247 0.000608 0.000631 0.00000 SCALE2 0.000000 0.017258 0.000631 0.00000 SCALE3 0.000000 0.000000 0.017270 0.00000