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HEADER LIPASE 02-SEP-97 5LIP
TITLE PSEUDOMONAS LIPASE COMPLEXED WITH RC-(RP,
TITLE 2 SP)-1,2-DIOCTYLCARBAMOYLGLYCERO-3-O-OCTYLPHOSPHONATE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRIACYL-GLYCEROL HYDROLASE;
COMPND 3 CHAIN: NULL;
COMPND 4 SYNONYM: LIPASE;
COMPND 5 EC: 3.1.1.3;
COMPND 6 ENGINEERED: YES;
COMPND 7 BIOLOGICAL_UNIT: MONOMER
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SP.;
SOURCE 3 ATCC: 21808;
SOURCE 4 CELLULAR_LOCATION: EXTRACELLULAR;
SOURCE 5 PLASMID: PHES12;
SOURCE 6 EXPRESSION_SYSTEM: PSEUDOMONAS SP.;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: 21808;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIUM;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: ESCHERICHIA COLI;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHES12
SOURCE 11 OTHER DETAILS: RENAMED ORGANISM BURKHOLDERIA CEPACIA
KEYWDS LIPASE, PSEUDOMONADACEAE, COVALENT INTERMEDIATE,
KEYWDS 2 TRIGLYCERIDE ANALOGUE, ENANTIOSELECTIVITY
EXPDTA X-RAY DIFFRACTION
AUTHOR D.A.LANG,B.W.DIJKSTRA
REVDAT 1 19-AUG-98 5LIP 0
JRNL AUTH D.A.LANG,M.L.M.MANNESSE,G.DE HAAS,H.M.VERHEIJ,
JRNL AUTH 2 B.W.DIJKSTRA
JRNL TITL STRUCTURAL EVIDENCE FOR THE CHIRAL REGIO
JRNL TITL 2 SELECTIVITY OF THE LIPASE FROM PSEUDOMONAS SPEC.
JRNL TITL 3 ATCC 21808
JRNL REF TO BE PUBLISHED
JRNL REFN 0353
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.D.SCHRAG,Y.LI,M.CYGLER,D.LANG,T.BURGDORF,
REMARK 1 AUTH 2 H.J.HECHT,R.SCHMID,D.SCHOMBURG,T.J.RYDEL,
REMARK 1 AUTH 3 J.D.OLIVER,L.C.STRICKLAND,C.M.DUNAWAY,S.B.LARSON,
REMARK 1 AUTH 4 J.DAY,A.MCPHERSON
REMARK 1 TITL THE OPEN CONFORMATION OF A PSEUDOMONAS LIPASE
REMARK 1 REF STRUCTURE (LONDON) V. 5 187 1997
REMARK 1 REFN ASTM STRUE6 UK ISSN 0969-2126 2005
REMARK 1 REFERENCE 2
REMARK 1 AUTH M.KORDEL,B.HOFMANN,D.SCHOMBURG,R.D.SCHMID
REMARK 1 TITL EXTRACELLULAR LIPASE OF PSEUDOMONAS SP. STRAIN
REMARK 1 TITL 2 ATCC 21808: PURIFICATION, CHARACTERIZATION,
REMARK 1 TITL 3 CRYSTALLIZATION, AND PRELIMINARY X-RAY DIFFRACTION
REMARK 1 TITL 4 DATA
REMARK 1 REF J.BACTERIOL. V. 173 4836 1991
REMARK 1 REFN ASTM JOBAAY US ISSN 0021-9193 0767
REMARK 2
REMARK 2 RESOLUTION. 2.9 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.843
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.9
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.0
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.001
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.5
REMARK 3 NUMBER OF REFLECTIONS : 6221
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) : 0.206
REMARK 3 FREE R VALUE : 0.285
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.
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) : 2.9
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.03
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 623
REMARK 3 BIN R VALUE (WORKING SET) : 0.23
REMARK 3 BIN FREE R VALUE : 0.27
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 : 2335
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 39
REMARK 3 SOLVENT ATOMS : 4
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.0
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) : 0.2
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.0
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) : 0.013
REMARK 3 BOND ANGLES (DEGREES) : 1.98
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.6
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.70
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 : OCP.PRO
REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO
REMARK 3 TOPOLOGY FILE 2 : OCP.TOP
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE CIS-PEPTIDE BOND VISIBLE IN
REMARK 3 THE HIGH RESOLUTION STRUCTURES COULD NOT BE KEPT AT 2.9
REMARK 3 ANG.
REMARK 4
REMARK 4 5LIP COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 6
REMARK 6 THE STARTING MATERIAL FOR THE INHIBITOR WAS RC-(RP,SP)-1,2-
REMARK 6 DIOCTYLCARBAMOYL-GLYCERO-3-O-P-NITROPHENYL-
REMARK 6 OCTYLPHOSPHONATE. BY THE REACTION DESCRIBED IN THE JNRL
REMARK 6 ABOVE, THIS TURNED INTO
REMARK 6 RC-SP-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-OCTYLPHOSPHONATE,
REMARK 6 COVALENTLY BOUND TO THE PROTEIN.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : MAY-1996
REMARK 200 TEMPERATURE (KELVIN) : 120
REMARK 200 PH : 4.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DESY
REMARK 200 BEAMLINE : X31
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 : GRAPHITE
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 : 6515
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.9
REMARK 200 RESOLUTION RANGE LOW (A) : 20.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 3.4
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.092
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.1
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.9
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95
REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.158
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR
REMARK 200 REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 3LIP
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 14 % ISOPROPANOL, 0.020 M
REMARK 280 CACL2, 0.1 M ACETATE, PH 4
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 1/2+X,1/2+Y,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.36557
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.21047
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.36557
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.21047
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 3LIP
REMARK 700
REMARK 700 SHEET
REMARK 700 DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 3LIP
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ACT
REMARK 800 SITE_DESCRIPTION: ACTIVE SITE.
REMARK 800
REMARK 800 SITE_IDENTIFIER: OXY
REMARK 800 SITE_DESCRIPTION: OXYANION HOLE.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 REFERENCE: NAKANISHI ET AL. (1991): CLONING, SEQUENCING,
REMARK 999 REGULATION OF THE LIPASE GENE FROM PSEUDOMONAS SP. M 12-33,
REMARK 999 IN LIPASES: STRUCTURE, MECHANISM, GENETIC ENGINEERING. GBF
REMARK 999 MONOGRAPHS NO. 16 (ALBERGHINA, SCHMID, VERGER EDS.) VCH,
REMARK 999 WEINHEIM, PP. 263-266.
DBREF 5LIP 1 320 PDB 5LIP 5LIP 1 320
SEQRES 1 320 ALA ASP ASN TYR ALA ALA THR ARG TYR PRO ILE ILE LEU
SEQRES 2 320 VAL HIS GLY LEU THR GLY THR ASP LYS TYR ALA GLY VAL
SEQRES 3 320 LEU GLU TYR TRP TYR GLY ILE GLN GLU ASP LEU GLN GLN
SEQRES 4 320 ARG GLY ALA THR VAL TYR VAL ALA ASN LEU SER GLY PHE
SEQRES 5 320 GLN SER ASP ASP GLY PRO ASN GLY ARG GLY GLU GLN LEU
SEQRES 6 320 LEU ALA TYR VAL LYS THR VAL LEU ALA ALA THR GLY ALA
SEQRES 7 320 THR LYS VAL ASN LEU VAL GLY HIS SER GLN GLY GLY LEU
SEQRES 8 320 THR SER ARG TYR VAL ALA ALA VAL ALA PRO ASP LEU VAL
SEQRES 9 320 ALA SER VAL THR THR ILE GLY THR PRO HIS ARG GLY SER
SEQRES 10 320 GLU PHE ALA ASP PHE VAL GLN GLY VAL LEU ALA TYR ASP
SEQRES 11 320 PRO THR GLY LEU SER SER THR VAL ILE ALA ALA PHE VAL
SEQRES 12 320 ASN VAL PHE GLY ILE LEU THR SER SER SER ASN ASN THR
SEQRES 13 320 ASN GLN ASP ALA LEU ALA ALA LEU LYS THR LEU THR THR
SEQRES 14 320 ALA GLN ALA ALA THR TYR ASN GLN ASN TYR PRO SER ALA
SEQRES 15 320 GLY LEU GLY ALA PRO GLY SER CYS GLN THR GLY ALA PRO
SEQRES 16 320 THR GLU THR VAL GLY GLY ASN THR HIS LEU LEU TYR SER
SEQRES 17 320 TRP ALA GLY THR ALA ILE GLN PRO THR ILE SER VAL PHE
SEQRES 18 320 GLY VAL THR GLY ALA THR ASP THR SER THR ILE PRO LEU
SEQRES 19 320 VAL ASP PRO ALA ASN ALA LEU ASP PRO SER THR LEU ALA
SEQRES 20 320 LEU PHE GLY THR GLY THR VAL MET VAL ASN ARG GLY SER
SEQRES 21 320 GLY GLN ASN ASP GLY VAL VAL SER LYS CYS SER ALA LEU
SEQRES 22 320 TYR GLY GLN VAL LEU SER THR SER TYR LYS TRP ASN HIS
SEQRES 23 320 LEU ASP GLU ILE ASN GLN LEU LEU GLY VAL ARG GLY ALA
SEQRES 24 320 ASN ALA GLU ASP PRO VAL ALA VAL ILE ARG THR HIS ALA
SEQRES 25 320 ASN ARG LEU LYS LEU ALA GLY VAL
HET CA 321 1
HET OCP 400 38
HETNAM CA CALCIUM ION
HETNAM OCP RC-SP-1,2-DIOCTYLCARBAMOYL-GLYCERO-3-O-OCTYL
HETNAM 2 OCP PHOSPHONATE
FORMUL 2 CA CA1 2+
FORMUL 3 OCP C29 H58 N2 O6 P1
FORMUL 4 HOH *4(H2 O1)
HELIX 1 1 ILE 33 GLN 39 1 7
HELIX 2 2 ARG 61 THR 76 1 16
HELIX 3 3 GLY 89 VAL 99 5 11
HELIX 4 4 GLU 118 LEU 127 1 10
HELIX 5 5 LEU 134 THR 150 1 17
HELIX 6 6 ALA 160 THR 166 1 7
HELIX 7 7 THR 169 ASN 178 1 10
HELIX 8 8 ALA 238 LEU 241 5 4
HELIX 9 9 SER 244 VAL 256 1 13
HELIX 10 10 LYS 269 ALA 272 1 4
HELIX 11 11 PRO 304 ALA 318 1 15
SHEET 1 A1 6 VAL 44 VAL 46 0
SHEET 2 A1 6 PRO 10 VAL 14 1 N ILE 11 O TYR 45
SHEET 3 A1 6 VAL 81 HIS 86 1 N ASN 82 O PRO 10
SHEET 4 A1 6 VAL 104 ILE 110 1 N ALA 105 O VAL 81
SHEET 5 A1 6 THR 203 GLY 211 1 N LEU 205 O VAL 107
SHEET 6 A1 6 THR 196 THR 198 -1 N GLU 197 O HIS 204
SHEET 1 A2 6 VAL 44 VAL 46 0
SHEET 2 A2 6 PRO 10 VAL 14 1 N ILE 11 O TYR 45
SHEET 3 A2 6 VAL 81 HIS 86 1 N ASN 82 O PRO 10
SHEET 4 A2 6 VAL 104 ILE 110 1 N ALA 105 O VAL 81
SHEET 5 A2 6 THR 203 GLY 211 1 N LEU 205 O VAL 107
SHEET 6 A2 6 GLN 276 TYR 282 1 N SER 279 O SER 208
SHEET 1 B 2 LYS 22 TYR 23 0
SHEET 2 B 2 LEU 27 GLU 28 -1 N LEU 27 O TYR 23
SHEET 1 C 2 ILE 214 VAL 220 0
SHEET 2 C 2 VAL 223 ASP 228 -1 N THR 227 O GLN 215
LINK P1 OCP 400 OG SER 87
SITE 1 ACT 3 SER 87 HIS 286 ASP 264
SITE 1 OXY 2 LEU 17 GLN 88
CRYST1 88.730 46.420 83.950 90.00 121.23 90.00 C 1 2 1 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 0.011270 0.000000 0.006834 0.00000
SCALE2 0.000000 0.021542 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013930 0.00000 |