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HEADER HYDROLASE 02-MAY-00 1EX9
TITLE CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LIPASE
TITLE 2 COMPLEXED WITH RC-(RP,SP)-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-
TITLE 3 OCTYLPHOSPHONATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LACTONIZING LIPASE;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: TRIACYL-GLYCEROL LIPASE;
COMPND 5 EC: 3.1.1.3;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA;
SOURCE 3 ORGANISM_COMMON: BACTERIA;
SOURCE 4 EXPRESSION_SYSTEM: PSEUDOMONAS SP;
SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA;
SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PEL11
KEYWDS LIPASE, ALPHA-BETA HYDROLASE FOLD, PSEUDOMONAS, PHOSPHONATE
KEYWDS 2 INHIBITOR
EXPDTA X-RAY DIFFRACTION
AUTHOR M.NARDINI,D.A.LANG,K.LIEBETON,K.-E.JAEGER,B.W.DIJKSTRA
REVDAT 1 18-OCT-00 1EX9 0
JRNL AUTH M.NARDINI,D.A.LANG,K.LIEBETON,K.-E.JAEGER,
JRNL AUTH 2 B.W.DIJKSTRA
JRNL TITL CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA LIPASE
JRNL TITL 2 IN THE OPEN CONFORMATION. THE PROTOTYPE FOR FAMILY
JRNL TITL 3 I.1 OF BACTERIAL LIPASES
JRNL REF J.BIOL.CHEM. V. 275 31219 2000
JRNL REFN ASTM JBCHA3 US ISSN 0021-9258
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 2.54 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
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 : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.54
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.55
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 34304
REMARK 3
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.195
REMARK 3 FREE R VALUE : 0.245
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 413
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 : 2125
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 39
REMARK 3 SOLVENT ATOMS : 112
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 0.00
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) : 0.012
REMARK 3 BOND ANGLES (DEGREES) : 1.53
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
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: NULL
REMARK 4
REMARK 4 1EX9 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-2000.
REMARK 100 THE RCSB ID CODE IS RCSB010989.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 29-JUL-1998
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 5.60
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 : BW7B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
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 : TRUNCATE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8772
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540
REMARK 200 RESOLUTION RANGE LOW (A) : 28.550
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 200 DATA REDUNDANCY : 3.900
REMARK 200 R MERGE (I) : 0.11900
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) : 2.54
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 28.55
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.00
REMARK 200 R MERGE FOR SHELL (I) : 0.33600
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: MOLECULAR
REMARK 200 REPLACEMENT
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 (%): 44.0
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, CALCIUM CHLORIDE, CITRATE
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 1/2-X,-Y,1/2+Z
REMARK 290 3555 -X,1/2+Y,1/2-Z
REMARK 290 4555 1/2+X,1/2-Y,-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 22.73500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.01700
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.48150
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.01700
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.73500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.48150
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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
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 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 M RES CSSEQI PSI PHI
REMARK 500 SER A 82 57.50 -111.75
REMARK 525
REMARK 525 SOLVENT
REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED
REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE
REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL
REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 0 HOH 427 DISTANCE = 6.57 ANGSTROMS
REMARK 525 0 HOH 443 DISTANCE = 7.24 ANGSTROMS
REMARK 525 0 HOH 467 DISTANCE = 5.04 ANGSTROMS
REMARK 525 0 HOH 475 DISTANCE = 5.32 ANGSTROMS
REMARK 525 0 HOH 508 DISTANCE = 6.97 ANGSTROMS
DBREF 1EX9 A 1 285 SWS P26876 LIP_PSEAE 27 311
SEQRES 1 A 285 SER THR TYR THR GLN THR LYS TYR PRO ILE VAL LEU ALA
SEQRES 2 A 285 HIS GLY MET LEU GLY PHE ASP ASN ILE LEU GLY VAL ASP
SEQRES 3 A 285 TYR TRP PHE GLY ILE PRO SER ALA LEU ARG ARG ASP GLY
SEQRES 4 A 285 ALA GLN VAL TYR VAL THR GLU VAL SER GLN LEU ASP THR
SEQRES 5 A 285 SER GLU VAL ARG GLY GLU GLN LEU LEU GLN GLN VAL GLU
SEQRES 6 A 285 GLU ILE VAL ALA LEU SER GLY GLN PRO LYS VAL ASN LEU
SEQRES 7 A 285 ILE GLY HIS SER HIS GLY GLY PRO THR ILE ARG TYR VAL
SEQRES 8 A 285 ALA ALA VAL ARG PRO ASP LEU ILE ALA SER ALA THR SER
SEQRES 9 A 285 VAL GLY ALA PRO HIS LYS GLY SER ASP THR ALA ASP PHE
SEQRES 10 A 285 LEU ARG GLN ILE PRO PRO GLY SER ALA GLY GLU ALA VAL
SEQRES 11 A 285 LEU SER GLY LEU VAL ASN SER LEU GLY ALA LEU ILE SER
SEQRES 12 A 285 PHE LEU SER SER GLY SER THR GLY THR GLN ASN SER LEU
SEQRES 13 A 285 GLY SER LEU GLU SER LEU ASN SER GLU GLY ALA ALA ARG
SEQRES 14 A 285 PHE ASN ALA LYS TYR PRO GLN GLY ILE PRO THR SER ALA
SEQRES 15 A 285 CYS GLY GLU GLY ALA TYR LYS VAL ASN GLY VAL SER TYR
SEQRES 16 A 285 TYR SER TRP SER GLY SER SER PRO LEU THR ASN PHE LEU
SEQRES 17 A 285 ASP PRO SER ASP ALA PHE LEU GLY ALA SER SER LEU THR
SEQRES 18 A 285 PHE LYS ASN GLY THR ALA ASN ASP GLY LEU VAL GLY THR
SEQRES 19 A 285 CYS SER SER HIS LEU GLY MET VAL ILE ARG ASP ASN TYR
SEQRES 20 A 285 ARG MET ASN HIS LEU ASP GLU VAL ASN GLN VAL PHE GLY
SEQRES 21 A 285 LEU THR SER LEU PHE GLU THR SER PRO VAL SER VAL TYR
SEQRES 22 A 285 ARG GLN HIS ALA ASN ARG LEU LYS ASN ALA SER LEU
MODRES 1EX9 SER A 82 SER COVALENT LINK WITH OCP
HET CA A 286 1
HET OCP A 382 38
HETNAM CA CALCIUM ION
HETNAM OCP OCTYL-PHOSPHINIC ACID 1,2-BIS-OCTYLCARBAMOYLOXY-ETHYL
HETNAM 2 OCP ESTER
FORMUL 2 CA CA1 2+
FORMUL 3 OCP C29 H59 N2 O7 P1
FORMUL 4 HOH *112(H2 O1)
HELIX 1 1 GLY A 30 ASP A 38 1 9
HELIX 2 2 THR A 52 GLY A 72 1 21
HELIX 3 3 HIS A 83 ARG A 95 1 13
HELIX 4 4 SER A 112 LEU A 118 1 7
HELIX 5 5 ARG A 119 ILE A 121 5 3
HELIX 6 6 SER A 125 GLY A 148 1 24
HELIX 7 7 ASN A 154 ASN A 163 1 10
HELIX 8 8 ASN A 163 TYR A 174 1 12
HELIX 9 9 PRO A 210 SER A 219 1 10
HELIX 10 10 LEU A 220 PHE A 222 5 3
HELIX 11 11 LEU A 252 ASN A 256 5 5
HELIX 12 12 SER A 268 ALA A 283 1 16
SHEET 1 A 6 VAL A 42 THR A 45 0
SHEET 2 A 6 ILE A 10 ALA A 13 1 O ILE A 10 N TYR A 43
SHEET 3 A 6 VAL A 76 HIS A 81 1 O ASN A 77 N VAL A 11
SHEET 4 A 6 ILE A 99 VAL A 105 1 N ALA A 100 O VAL A 76
SHEET 5 A 6 VAL A 193 TRP A 198 1 O SER A 194 N ALA A 102
SHEET 6 A 6 LYS A 189 VAL A 190 -1 N VAL A 190 O VAL A 193
SHEET 1 B 6 VAL A 42 THR A 45 0
SHEET 2 B 6 ILE A 10 ALA A 13 1 O ILE A 10 N TYR A 43
SHEET 3 B 6 VAL A 76 HIS A 81 1 O ASN A 77 N VAL A 11
SHEET 4 B 6 ILE A 99 VAL A 105 1 N ALA A 100 O VAL A 76
SHEET 5 B 6 VAL A 193 TRP A 198 1 O SER A 194 N ALA A 102
SHEET 6 B 6 MET A 241 VAL A 242 1 N MET A 241 O TYR A 195
SHEET 1 C 2 ASN A 21 ILE A 22 0
SHEET 2 C 2 VAL A 25 ASP A 26 -1 O VAL A 25 N ILE A 22
SSBOND 1 CYS A 183 CYS A 235
LINK OG SER A 82 P1 OCP A 382
CISPEP 1 GLN A 257 VAL A 258 0 -0.44
CRYST1 45.470 50.963 110.034 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 0.021993 0.000000 0.000000 0.00000
SCALE2 0.000000 0.019622 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009088 0.00000
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