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HEADER HYDROLASE 13-DEC-96 2LIP
TITLE PSEUDOMONAS LIPASE OPEN CONFORMATION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LIPASE;
COMPND 3 CHAIN: NULL;
COMPND 4 SYNONYM: TRIACYLGLYCEROL HYDROLASE;
COMPND 5 EC: 3.1.1.3;
COMPND 6 BIOLOGICAL_UNIT: MONOMER
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS CEPACIA;
SOURCE 3 OTHER_DETAILS: COMMERCIAL PREP FROM GENZYME CORPORATION
KEYWDS HYDROLASE, LIPASE, PSEUDOMONAS, CATALYTIC TRIAD
EXPDTA X-RAY DIFFRACTION
AUTHOR J.D.SCHRAG,M.CYGLER
REVDAT 1 12-MAR-97 2LIP 0
JRNL AUTH J.D.SCHRAG,Y.LI,M.CYGLER,D.LANG,T.BURGDORF,
JRNL AUTH 2 H.-J.HECHT,R.SCHMID,D.SCHOMBURG,T.J.RYDEL,
JRNL AUTH 3 J.D.OLIVER,L.C.STRICKLAND,C.M.DUNAWAY,S.B.LARSON,
JRNL AUTH 4 J.DAY,A.MCPHERSON
JRNL TITL THE OPEN CONFORMATION OF A PSEUDOMONAS LIPASE
JRNL REF TO BE PUBLISHED REF NOW ASSIGNED AS
JRNL REFN 0353
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 2.1 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.1
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.0
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 999999.0
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 12694
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) : 0.163
REMARK 3 FREE R VALUE : 0.22
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.
REMARK 3 FREE R VALUE TEST SET COUNT : 1281
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006
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) : 2.1
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 924
REMARK 3 BIN R VALUE (WORKING SET) : 0.208
REMARK 3 BIN FREE R VALUE : 0.247
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 95
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2251
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 1
REMARK 3 SOLVENT ATOMS : 91
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) : 0.2
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) : 0.008
REMARK 3 BOND ANGLES (DEGREES) : 1.50
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.04
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.23
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) : NULL ; 2.0
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 3.0
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.0
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 3.0
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 : PARHCDSX.PRO
REMARK 3 PARAMETER FILE 2 : PARAM19.SOL
REMARK 3 PARAMETER FILE 3 : PARAM_CIS.PRO
REMARK 3 PARAMETER FILE 4 : PARAM19.ION
REMARK 3 TOPOLOGY FILE 1 : TOPHCDSX.PRO
REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL
REMARK 3 TOPOLOGY FILE 3 : TOPH_CIS.PRO
REMARK 3 TOPOLOGY FILE 4 : TOPH19.ION
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2LIP COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 6
REMARK 6 DENSITY FOR RESIDUES 19 - 27 IS FRAGMENTED AND POSITIONS
REMARK 6 ARE UNCERTAIN. MODELED POSITIONS ARE BEST GUESS. THE
REMARK 6 OCCUPANCIES WERE SET TO 0.2 INDICATE THE UNCERTAINTY.
REMARK 6 LYS 22 SEEMED CLEARER AND ITS SIDE CHAIN WAS INCLUDED,
REMARK 6 BUT STILL SHOULD BE REGARDED AS A GUESS.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 23-MAR-1994
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 8.5
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 : RU-300
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : COLLIMATOR
REMARK 200
REMARK 200 DETECTOR TYPE : RAXISII
REMARK 200 DETECTOR MANUFACTURER : RIGAKU
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : RAXISII(MSC)
REMARK 200 DATA SCALING SOFTWARE : RAXISII(MSC)
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14497
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.1
REMARK 200 RESOLUTION RANGE LOW (A) : 39.11
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 79.4
REMARK 200 DATA REDUNDANCY : 1.69
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.0603
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.12
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.1
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.2
REMARK 200 COMPLETENESS FOR SHELL (%) : 60.6
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.96
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR
REMARK 200 REPLACEMENT
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: PDB ENTRY 1TAH
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.4
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50% N-PROPANOL, 50 MM TRIS,
REMARK 280 PH 8.5, 291 K, HANGING DROP VAPOR DIFFUSION
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 45.74984
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.66976
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.74984
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.66976
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 THR 20 OG1 CG2
REMARK 470 ASP 21 CG OD1 OD2
REMARK 470 TYR 23 CG CD1 CE1 CZ CE2 CD2 OH
REMARK 470 VAL 26 CB CG1 CG2
REMARK 470 SER 219 CB OG
REMARK 470 VAL 220 CB CG1 CG2
REMARK 470 PHE 221 CB CG CD1 CE1 CZ CE2 CD2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 2LIP SWS P22088 1 - 44 NOT IN ATOMS LIST
REMARK 999
REMARK 999 THIS SEQUENCE MATCHES THAT REFERENCED IN
REMARK 999 NAKANISHI ET AL. (1991) IN LIPASES: STRUCTURE,
REMARK 999 MECHANISM, GENETIC ENGINEERING. GBF MONOGRAPHS NO. 16
REMARK 999 (ALBERGHINA, SCHMID, VERGER, EDS.) VCH, WEINHEIM, PP.
REMARK 999 263-266 EXCEPT FOR RESIDUE 283 WHICH IS K RATHER THAN L.
DBREF 2LIP 1 320 SWS P22088 LIP_BURCE 45 364
SEQADV 2LIP ASP 2 SWS P22088 ALA 46 CONFLICT
SEQADV 2LIP ASN 3 SWS P22088 GLY 47 CONFLICT
SEQADV 2LIP THR 18 SWS P22088 SER 62 CONFLICT
SEQADV 2LIP ARG 40 SWS P22088 ASN 84 CONFLICT
SEQADV 2LIP THR 92 SWS P22088 SER 136 CONFLICT
SEQADV 2LIP GLY 125 SWS P22088 ASP 169 CONFLICT
SEQADV 2LIP THR 137 SWS P22088 SER 181 CONFLICT
SEQADV 2LIP ASN 154 SWS P22088 HIS 198 CONFLICT
SEQADV 2LIP LYS 165 SWS P22088 GLN 209 CONFLICT
SEQADV 2LIP GLN 171 SWS P22088 ARG 215 CONFLICT
SEQADV 2LIP ILE 218 SWS P22088 LEU 262 CONFLICT
SEQADV 2LIP ILE 232 SWS P22088 LEU 276 CONFLICT
SEQADV 2LIP ALA 240 SWS P22088 VAL 284 CONFLICT
SEQADV 2LIP PRO 243 SWS P22088 LEU 287 CONFLICT
SEQADV 2LIP VAL 256 SWS P22088 ILE 300 CONFLICT
SEQADV 2LIP VAL 266 SWS P22088 LEU 310 CONFLICT
SEQADV 2LIP GLN 276 SWS P22088 LYS 320 CONFLICT
SEQADV 2LIP ASN 300 SWS P22088 TYR 344 CONFLICT
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 400 1
HETNAM CA CALCIUM ION
FORMUL 2 CA CA1 2+
FORMUL 3 HOH *91(H2 O1)
HELIX 1 1 ILE 33 ARG 40 1 8
HELIX 2 2 ARG 61 THR 76 1 16
HELIX 3 3 SER 87 VAL 99 5 13
HELIX 4 4 PRO 101 LEU 103 5 3
HELIX 5 5 GLU 118 TYR 129 1 12
HELIX 6 6 LEU 134 THR 150 1 17
HELIX 7 7 ALA 160 THR 166 1 7
HELIX 8 8 THR 169 ASN 178 1 10
HELIX 9 9 PRO 237 LEU 241 5 5
HELIX 10 10 PRO 243 ARG 258 1 16
HELIX 11 11 LYS 269 ALA 272 1 4
HELIX 12 12 PRO 304 ALA 318 1 15
SHEET 1 A 6 VAL 44 VAL 46 0
SHEET 2 A 6 PRO 10 VAL 14 1 N ILE 11 O TYR 45
SHEET 3 A 6 VAL 81 HIS 86 1 N ASN 82 O PRO 10
SHEET 4 A 6 VAL 104 ILE 110 1 N ALA 105 O VAL 81
SHEET 5 A 6 ASN 202 TRP 209 1 N LEU 205 O VAL 107
SHEET 6 A 6 GLN 276 SER 279 1 N GLN 276 O SER 208
SHEET 1 B 2 ILE 214 PRO 216 0
SHEET 2 B 2 ALA 226 ASP 228 -1 N THR 227 O GLN 215
SHEET 1 C 2 ASN 202 TRP 209 0
SHEET 2 C 2 THR 196 VAL 199 -1 N VAL 199 O ASN 202
SSBOND 1 CYS 190 CYS 270
LINK CA CA 400 OD2 ASP 242
LINK CA CA 400 O GLN 292
LINK CA CA 400 O VAL 296
CISPEP 1 GLN 292 LEU 293 0 -0.48
SITE 1 CAT 3 SER 87 ASP 264 HIS 286
CRYST1 91.500 47.340 85.220 90.00 121.25 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 0.010929 0.000000 0.006632 0.00000
SCALE2 0.000000 0.021124 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013726 0.00000 |