HEADER HYDROLASE 05-MAR-03 1O2E TITLE STRUCTURE OF THE TRIPLE MUTANT (K53,56,120M) + ANISIC ACID COMPLEX OF TITLE 2 PHOSPHOLIPASE A2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHATIDYLCHOLINE 2- ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE COMPND 5 A2; COMPND 6 EC: 3.1.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTO-A2MBL21 KEYWDS ALPHA HELIX, BETA SHEET, TRIPLE MUTANT, ANISIC ACID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SEKAR,D.VELMURUGAN,M.D.TSAI REVDAT 7 09-OCT-24 1O2E 1 REMARK REVDAT 6 27-DEC-23 1O2E 1 REMARK REVDAT 5 27-OCT-21 1O2E 1 REMARK SEQADV LINK REVDAT 4 04-OCT-17 1O2E 1 REMARK REVDAT 3 24-FEB-09 1O2E 1 VERSN REVDAT 2 21-SEP-04 1O2E 1 JRNL REVDAT 1 09-SEP-03 1O2E 0 JRNL AUTH K.SEKAR,S.VAIJAYANTHI MALA,M.YOGAVEL,D.VELMURUGAN,M.J.POI, JRNL AUTH 2 B.S.VISHWANATH,T.V.GOWDA,A.A.JEYAPRAKASH,M.D.TSAI JRNL TITL CRYSTAL STRUCTURES OF THE FREE AND ANISIC ACID BOUND TRIPLE JRNL TITL 2 MUTANT OF PHOSPHOLIPASE A2. JRNL REF J.MOL.BIOL. V. 333 367 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 14529623 JRNL DOI 10.1016/J.JMB.2003.08.032 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 3957 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 240 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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: CNS 1.1 REMARK 4 REMARK 4 1O2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000001718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.2 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 : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3957 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLECULAR REPLACEMENT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS BUFFER, MPD,70% MPD REMARK 280 RESERVOIR,17-20MG/ML PROT,5 MM CACL2, 1 MICROLITRE OF ANISIC REMARK 280 ACID, PH 7.2, VAPOR DIFFUSION METHOD, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.22667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.45333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.45333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.22667 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 MET A 120 9.57 -55.57 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 124 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 28 O REMARK 620 2 GLY A 30 O 84.3 REMARK 620 3 GLY A 32 O 90.4 75.7 REMARK 620 4 ASP A 49 OD2 97.2 156.3 80.6 REMARK 620 5 ASP A 49 OD1 113.8 149.3 126.1 50.4 REMARK 620 6 HOH A 229 O 165.6 85.3 77.4 88.5 79.9 REMARK 620 7 ANN A 401 O1 87.2 79.0 154.7 124.7 77.4 100.5 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 124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MKT RELATED DB: PDB REMARK 900 1MKT IS THE TRIGONAL RECOMBINANT PHOSPHOLIPASE ENZYME WITHOUT REMARK 900 MUTATION DBREF 1O2E A 1 123 UNP P00593 PA21B_BOVIN 23 145 SEQADV 1O2E MET A 53 UNP P00593 LYS 75 ENGINEERED MUTATION SEQADV 1O2E MET A 56 UNP P00593 LYS 78 ENGINEERED MUTATION SEQADV 1O2E MET A 120 UNP P00593 LYS 142 ENGINEERED MUTATION SEQRES 1 A 123 ALA LEU TRP GLN PHE ASN GLY MET ILE LYS CYS LYS ILE SEQRES 2 A 123 PRO SER SER GLU PRO LEU LEU ASP PHE ASN ASN TYR GLY SEQRES 3 A 123 CYS TYR CYS GLY LEU GLY GLY SER GLY THR PRO VAL ASP SEQRES 4 A 123 ASP LEU ASP ARG CYS CYS GLN THR HIS ASP ASN CYS TYR SEQRES 5 A 123 MET GLN ALA MET LYS LEU ASP SER CYS LYS VAL LEU VAL SEQRES 6 A 123 ASP ASN PRO TYR THR ASN ASN TYR SER TYR SER CYS SER SEQRES 7 A 123 ASN ASN GLU ILE THR CYS SER SER GLU ASN ASN ALA CYS SEQRES 8 A 123 GLU ALA PHE ILE CYS ASN CYS ASP ARG ASN ALA ALA ILE SEQRES 9 A 123 CYS PHE SER LYS VAL PRO TYR ASN LYS GLU HIS LYS ASN SEQRES 10 A 123 LEU ASP MET LYS ASN CYS HET CA A 124 1 HET ANN A 401 11 HETNAM CA CALCIUM ION HETNAM ANN 4-METHOXYBENZOIC ACID HETSYN ANN P-ANISIC ACID FORMUL 2 CA CA 2+ FORMUL 3 ANN C8 H8 O3 FORMUL 4 HOH *43(H2 O) HELIX 1 1 ALA A 1 ILE A 13 1 13 HELIX 2 2 GLU A 17 PHE A 22 1 6 HELIX 3 3 ASP A 39 MET A 56 1 18 HELIX 4 4 LEU A 58 LEU A 64 1 7 HELIX 5 5 ASN A 89 SER A 107 1 19 HELIX 6 6 ASN A 112 LYS A 116 5 5 HELIX 7 7 ASP A 119 CYS A 123 5 5 SHEET 1 A 2 TYR A 75 SER A 78 0 SHEET 2 A 2 GLU A 81 CYS A 84 -1 O THR A 83 N SER A 76 SSBOND 1 CYS A 11 CYS A 77 1555 1555 2.04 SSBOND 2 CYS A 27 CYS A 123 1555 1555 2.03 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.04 SSBOND 4 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.03 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.03 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.03 LINK O TYR A 28 CA CA A 124 1555 1555 2.24 LINK O GLY A 30 CA CA A 124 1555 1555 2.42 LINK O GLY A 32 CA CA A 124 1555 1555 2.34 LINK OD2 ASP A 49 CA CA A 124 1555 1555 2.40 LINK OD1 ASP A 49 CA CA A 124 1555 1555 2.70 LINK CA CA A 124 O HOH A 229 1555 1555 2.57 LINK CA CA A 124 O1 ANN A 401 1555 1555 2.32 SITE 1 AC1 6 TYR A 28 GLY A 30 GLY A 32 ASP A 49 SITE 2 AC1 6 HOH A 229 ANN A 401 SITE 1 AC2 9 PHE A 5 PRO A 18 LEU A 19 TYR A 28 SITE 2 AC2 9 GLY A 30 ASP A 49 TYR A 69 CA A 124 SITE 3 AC2 9 HOH A 228 CRYST1 46.610 46.610 102.680 90.00 90.00 120.00 P 31 2 1 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 0.021455 0.012387 0.000000 0.00000 SCALE2 0.000000 0.024774 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009739 0.00000