10 20 30 40 50 60 70 80 1PO8 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 14-JUN-03 1PO8
TITLE CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN KRAIT VENOM TITLE 2 PHOSPHOLIPASE A2 AND HEPTANOIC ACID AT 2.7 A RESOLUTION.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHOSPHOLIPASE A2; COMPND 5 EC: 3.1.1.4
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BUNGARUS CAERULEUS; SOURCE 3 ORGANISM_TAXID: 132961; SOURCE 4 OTHER_DETAILS: VENOM PROTEIN
KEYWDS PHOSPHOLIPASE A2, CRYSTAL STRUCTURE,INHIBITOR,COMPLEX, KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.SINGH,J.JAYASANKAR,S.SHARMA,P.KAUR,T.P.SINGH
REVDAT 2 24-FEB-09 1PO8 1 VERSN REVDAT 1 04-MAY-04 1PO8 0
JRNL AUTH G.SINGH,J.JAYASANKAR,S.SHARMA,P.KAUR,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN JRNL TITL 2 KRAIT VENOM PHOSPHOLIPASE A2 AND HEPTANOIC ACID AT JRNL TITL 3 2.7 A RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.71 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1786405.830 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 3380 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) : 0.207 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 180 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.023 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) : 2.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 473 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 32 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.063 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.89000 REMARK 3 B22 (A**2) : 1.89000 REMARK 3 B33 (A**2) : -3.78000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.44 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) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.73 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.40 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.92 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) : 1.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.980 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.600 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.490 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 54.08 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1PO8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-03. REMARK 100 THE RCSB ID CODE IS RCSB019462.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 8.5 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS 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 : 3380 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 90.1 REMARK 200 DATA REDUNDANCY : 2.340 REMARK 200 R MERGE (I) : 0.17000 REMARK 200 R SYM (I) : 0.17000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.34 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 REMARK 200 R SYM FOR SHELL (I) : 0.40300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 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 (%): 45.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M TRIS-HCL, 2.4 M NACL, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 41.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.89500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.89500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.89500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.89500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.89500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.89500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.89500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.89500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.87500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 41.25000 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: 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 PRO A 20 -18.10 -48.14 REMARK 500 ASP A 39 -155.94 -134.50 REMARK 500 GLU A 74 114.69 -29.83 REMARK 500 SER A 82 -53.19 -127.16 REMARK 500 MET A 112 50.25 -150.72 REMARK 500 SER A 115 -3.18 57.22 REMARK 500 ASN A 117 -16.00 109.87 REMARK 500 CYS A 119 69.81 -102.79 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 178 DISTANCE = 5.64 ANGSTROMS
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 NA A 121 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 49 OD2 REMARK 620 2 TYR A 28 O 128.0 REMARK 620 3 GLY A 30 O 142.3 74.0 REMARK 620 4 GLY A 32 O 118.1 92.1 86.7 REMARK 620 5 ASP A 49 OD1 48.5 92.8 108.6 164.7 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 121 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SHV A 122
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FE5 RELATED DB: PDB REMARK 900 SEQUENCE AND CRYSTAL STRUCTURE OF A BASIC PHOSPHOLIPASE A2 REMARK 900 FROM COMMON KRAIT (BUNGARUS CAERULEUS) AT 2.4 RESOLUTION: REMARK 900 IDENTIFICATION AND CHARACTERIZATION OF ITS PHARMACOLOGICAL REMARK 900 SITES.
DBREF 1PO8 A 1 120 UNP Q9DF52 PA2K_BUNCE 20 137
SEQRES 1 A 118 ASN LEU TYR GLN LEU MET ASN MET ILE GLN CYS ALA ASN SEQRES 2 A 118 THR ARG THR TRP PRO SER TYR THR ASN TYR GLY CYS TYR SEQRES 3 A 118 CYS GLY LYS GLY GLY SER GLY THR PRO VAL ASP ASP LEU SEQRES 4 A 118 ASP ARG CYS CYS TYR THR HIS ASP HIS CYS TYR ASN ASP SEQRES 5 A 118 ALA LYS ASN ILE ASP GLY CYS ASN PRO VAL THR LYS THR SEQRES 6 A 118 TYR SER TYR THR CYS THR GLU PRO THR ILE THR CYS ASN SEQRES 7 A 118 ASP SER LYS ASP LYS CYS ALA ARG PHE VAL CYS ASP CYS SEQRES 8 A 118 ASP ARG THR ALA ALA ILE CYS PHE ALA LYS ALA PRO TYR SEQRES 9 A 118 ASN THR SER ASN VAL MET ILE ARG SER THR ASN SER CYS SEQRES 10 A 118 GLN
HET NA A 121 1 HET SHV A 122 9
HETNAM NA SODIUM ION HETNAM SHV HEPTANOIC ACID
FORMUL 2 NA NA 1+ FORMUL 3 SHV C7 H14 O2 FORMUL 4 HOH *61(H2 O)
HELIX 1 1 ASN A 1 ASN A 13 1 13 HELIX 2 2 TRP A 19 ASN A 24 1 6 HELIX 3 3 ASP A 39 LYS A 56 1 18 HELIX 4 4 ASP A 84 ALA A 104 1 21
SHEET 1 A 2 TYR A 70 THR A 73 0 SHEET 2 A 2 THR A 76 CYS A 79 -1 O THR 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 2.02 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.03 SSBOND 4 CYS A 44 CYS A 100 1555 1555 2.02 SSBOND 5 CYS A 51 CYS A 93 1555 1555 2.02 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 NA NA A 121 OD2 ASP A 49 1555 1555 2.54 LINK O TYR A 28 NA NA A 121 1555 1555 2.66 LINK O GLY A 30 NA NA A 121 1555 1555 2.70 LINK O GLY A 32 NA NA A 121 1555 1555 2.63 LINK OD1 ASP A 49 NA NA A 121 1555 1555 2.79
CISPEP 1 GLU A 74 PRO A 75 0 0.94
SITE 1 AC1 5 TYR A 28 GLY A 30 GLY A 32 GLY A 33 SITE 2 AC1 5 ASP A 49 SITE 1 AC2 7 CYS A 29 GLY A 30 LYS A 31 ASP A 40 SITE 2 AC2 7 ARG A 43 CYS A 45 HIS A 48
CRYST1 53.790 53.790 82.500 90.00 90.00 90.00 P 41 21 2 8
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 0.018591 0.000000 0.000000 0.00000
SCALE2 0.000000 0.018591 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012121 0.00000