HEADER HYDROLASE 10-SEP-97 1MKU TITLE CARBOXYLIC ESTER HYDROLASE, ORTHORHOMBIC FORM OF THE TRIPLE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE A2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: ORTHORHOMBIC FORM OF THE TRIPLE MUTANT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 CELL_LINE: BL21; SOURCE 6 ORGAN: PANCREAS; SOURCE 7 GENE: PRO-PLA2; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)-[PLYSS]; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PRO-PLA2; SOURCE 12 EXPRESSION_SYSTEM_GENE: PRO-PLA2 KEYWDS HYDROLASE, ENZYME, CARBOXYLIC ESTER HYDROLASE, ORTHORHOMBIC FORM EXPDTA X-RAY DIFFRACTION AUTHOR M.SUNDARALINGAM REVDAT 5 13-NOV-24 1MKU 1 REMARK REVDAT 4 03-APR-24 1MKU 1 REMARK REVDAT 3 03-NOV-21 1MKU 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1MKU 1 VERSN REVDAT 1 24-DEC-97 1MKU 0 JRNL AUTH K.SEKAR,B.Z.YU,J.ROGERS,J.LUTTON,X.LIU,X.CHEN,M.D.TSAI, JRNL AUTH 2 M.K.JAIN,M.SUNDARALINGAM JRNL TITL PHOSPHOLIPASE A2 ENGINEERING. STRUCTURAL AND FUNCTIONAL JRNL TITL 2 ROLES OF THE HIGHLY CONSERVED ACTIVE SITE RESIDUE JRNL TITL 3 ASPARTATE-99. JRNL REF BIOCHEMISTRY V. 36 3104 1997 JRNL REFN ISSN 0006-2960 JRNL PMID 9115986 JRNL DOI 10.1021/BI961576X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.HUANG,B.Z.YU,J.ROGERS,I.J.BYEON,K.SEKAR,X.CHEN, REMARK 1 AUTH 2 M.SUNDARALINGAM,M.D.TSAI,M.K.JAIN REMARK 1 TITL PHOSPHOLIPASE A2 ENGINEERING. DELETION OF THE C-TERMINUS REMARK 1 TITL 2 SEGMENT CHANGES SUBSTRATE SPECIFICITY AND UNCOUPLES CALCIUM REMARK 1 TITL 3 AND SUBSTRATE BINDING AT THE ZWITTERIONIC INTERFACE REMARK 1 REF BIOCHEMISTRY V. 35 12164 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.P.NOEL,C.A.BINGMAN,T.L.DENG,C.M.DUPUREUR,K.J.HAMILTON, REMARK 1 AUTH 2 R.T.JIANG,J.G.KWAK,C.SEKHARUDU,M.SUNDARALINGAM,M.D.TSAI REMARK 1 TITL PHOSPHOLIPASE A2 ENGINEERING. X-RAY STRUCTURAL AND REMARK 1 TITL 2 FUNCTIONAL EVIDENCE FOR THE INTERACTION OF LYSINE-56 WITH REMARK 1 TITL 3 SUBSTRATES REMARK 1 REF BIOCHEMISTRY V. 30 11801 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 9538 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) : 0.196 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 46.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 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 : 955 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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) : 0.20 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS IIC REMARK 200 DATA SCALING SOFTWARE : R-AXIS II REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 8.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.07000 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.20700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: THE ATOMIC COORDINATES OF REMARK 200 THE NEW HIGH RESOLUTION REFINEMENT OF THE TRIGONAL FORM OF THE REMARK 200 NATIVE ENZYME WERE USED AS THE STARTING MODEL (PDB CODE: 1MKT). REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: WILD TYPE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY THE HANGING REMARK 280 DROP VAPOR DIFFUSION METHOD, PH 7.2, VAPOR DIFFUSION - HANGING REMARK 280 DROP, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 23.35500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.01500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 19.01500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.35500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.72500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 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 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 LEU A 64 -24.08 177.60 REMARK 500 VAL A 65 -14.34 65.44 REMARK 500 ASN A 71 104.19 -59.89 REMARK 500 PHE A 73 173.67 176.38 REMARK 500 ASN A 79 69.42 12.09 REMARK 500 LYS A 120 4.57 -57.02 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 90.7 REMARK 620 3 GLY A 32 O 98.7 86.1 REMARK 620 4 ASP A 49 OD1 105.6 137.9 127.6 REMARK 620 5 ASP A 49 OD2 98.5 164.2 79.9 51.4 REMARK 620 6 HOH A 235 O 76.1 71.9 157.2 74.8 122.7 REMARK 620 7 HOH A 236 O 170.5 83.0 88.0 74.9 89.2 95.1 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 DBREF 1MKU A 1 123 UNP P00593 PA21B_BOVIN 23 145 SEQADV 1MKU PHE A 52 UNP P00593 TYR 74 ENGINEERED MUTATION SEQADV 1MKU PHE A 73 UNP P00593 TYR 95 ENGINEERED MUTATION SEQADV 1MKU ASN A 99 UNP P00593 ASP 121 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 PHE SEQRES 5 A 123 LYS GLN ALA LYS LYS LEU ASP SER CYS LYS VAL LEU VAL SEQRES 6 A 123 ASP ASN PRO TYR THR ASN ASN PHE 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 ASN 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 LYS LYS ASN CYS HET CA A 124 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *80(H2 O) HELIX 1 1 LEU A 2 LYS A 12 1 11 HELIX 2 2 PRO A 18 ASP A 21 1 4 HELIX 3 3 ASP A 40 LYS A 57 1 18 HELIX 4 4 ASP A 59 LYS A 62 1 4 HELIX 5 5 ALA A 90 LYS A 108 1 19 HELIX 6 6 LYS A 113 HIS A 115 5 3 SHEET 1 A 2 TYR A 75 SER A 78 0 SHEET 2 A 2 GLU A 81 CYS A 84 -1 N THR A 83 O SER A 76 SSBOND 1 CYS A 11 CYS A 77 1555 1555 2.02 SSBOND 2 CYS A 27 CYS A 123 1555 1555 2.01 SSBOND 3 CYS A 29 CYS A 45 1555 1555 2.01 SSBOND 4 CYS A 44 CYS A 105 1555 1555 2.03 SSBOND 5 CYS A 51 CYS A 98 1555 1555 2.01 SSBOND 6 CYS A 61 CYS A 91 1555 1555 2.05 SSBOND 7 CYS A 84 CYS A 96 1555 1555 2.01 LINK O TYR A 28 CA CA A 124 1555 1555 2.04 LINK O GLY A 30 CA CA A 124 1555 1555 2.48 LINK O GLY A 32 CA CA A 124 1555 1555 2.32 LINK OD1 ASP A 49 CA CA A 124 1555 1555 2.60 LINK OD2 ASP A 49 CA CA A 124 1555 1555 2.47 LINK CA CA A 124 O HOH A 235 1555 1555 2.58 LINK CA CA A 124 O HOH A 236 1555 1555 2.57 SITE 1 AC1 6 TYR A 28 GLY A 30 GLY A 32 ASP A 49 SITE 2 AC1 6 HOH A 235 HOH A 236 CRYST1 46.710 65.450 38.030 90.00 90.00 90.00 P 21 21 21 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 0.021409 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015279 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026295 0.00000