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HEADER HYDROLASE 31-JUL-98 1BN7
TITLE HALOALKANE DEHALOGENASE FROM A RHODOCOCCUS SPECIES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HALOALKANE DEHALOGENASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 3.8.1.5;
COMPND 5 ENGINEERED: YES;
COMPND 6 BIOLOGICAL_UNIT: MONOMER
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS SP.;
SOURCE 3 COLLECTION: ATCC 55388;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI
KEYWDS DEHALOGENASE, ALPHA/BETA-HYDROLASE, DHLA, CRYSTAL STRUCTURE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.NEWMAN,T.S.PEAT,R.RICHARD,L.KAN,P.E.SWANSON,J.A.AFFHOLTER,
AUTHOR 2 I.H.HOLMES,J.F.SCHINDLER,C.J.UNKEFER,T.C.TERWILLIGER
REVDAT 1 18-FEB-00 1BN7 0
JRNL AUTH J.NEWMAN,T.S.PEAT,R.RICHARD,L.KAN,P.E.SWANSON,
JRNL AUTH 2 J.A.AFFHOLTER,I.H.HOLMES,J.F.SCHINDLER,C.J.UNKEFER,
JRNL AUTH 3 T.C.TERWILLIGER
JRNL TITL HALOALKANE DEHALOGENASES: STRUCTURE OF A
JRNL TITL 2 RHODOCOCCUS ENZYME
JRNL REF BIOCHEMISTRY V. 38 16105 1999
JRNL REFN ASTM BICHAW US ISSN 0006-2960
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.5 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 0.3
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,
REMARK 3 GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,
REMARK 3 PANNU,READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : MLF
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.5
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.0
REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.4
REMARK 3 NUMBER OF REFLECTIONS : 51658
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) : 0.158
REMARK 3 FREE R VALUE : 0.178
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5
REMARK 3 FREE R VALUE TEST SET COUNT : 2593
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.4
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7939
REMARK 3 BIN R VALUE (WORKING SET) : 0.16
REMARK 3 BIN FREE R VALUE : 0.198
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.4
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 449
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2310
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 4
REMARK 3 SOLVENT ATOMS : 369
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 12.6
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.7
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.20
REMARK 3 B22 (A**2) : 0.03
REMARK 3 B33 (A**2) : -0.23
REMARK 3 B12 (A**2) : 0.0
REMARK 3 B13 (A**2) : 0.0
REMARK 3 B23 (A**2) : 0.0
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.13
REMARK 3 ESD FROM SIGMAA (A) : 0.04
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.0
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.15
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.08
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.021
REMARK 3 BOND ANGLES (DEGREES) : 1.8
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.4
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.31
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) : 0.26 ; 1.50
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.45 ; 2.0
REMARK 3 SIDE-CHAIN BOND (A**2) : 0.18 ; 2.0
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.31 ; 2.5
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : 0.415
REMARK 3 BSOL : 55.7
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 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM
REMARK 3 PARAMETER FILE 3 : ACT.PARAM
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : ACT.TOP
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 3 CUTOFF HIGH (ABS(F)) : 1432151.63
REMARK 4
REMARK 4 1BN7 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 6
REMARK 6 DID NOT SEE ANY OF THE C-TERMINAL EXFLAG TAG
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : APR-1998
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X8C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.8157
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 : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52882
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.50
REMARK 200 RESOLUTION RANGE LOW (A) : 50.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8
REMARK 200 DATA REDUNDANCY : 3.4
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.032
REMARK 200 FOR THE DATA SET : 11.2
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56
REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5
REMARK 200 DATA REDUNDANCY IN SHELL : 3.1
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.093
REMARK 200 FOR SHELL : 7.9
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.8
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS:
REMARK 280 1 UL PROTEIN (5MG/ML PROTEIN IN 150MM AMMONIUM SULFATE,
REMARK 280 10MM TRISSO4 PH 7.5, 1MM EDTA) +1 UL RESERVOIR OVER
REMARK 280 20-25% PEG 1.5K, 0.2M NAACETATE, 0.1M MES PH 5.5 AT 8C
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
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 46.81648
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.94567
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.81648
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.94567
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 12
REMARK 465 SER A 13
REMARK 465 GLU A 14
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD RESIDUES
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 FIRST 11 RESIDUES ARE A HIS-TAG, THE LAST 12 ARE AN EXFLAG
DBREF 1BN7 A 12 304 GB 3114657 AF060871 1 293
SEQADV 1BN7 VAL A 183 GB 3114657 ALA A 172 CONFLICT
SEQADV 1BN7 ILE A 220 GB 3114657 LEU A 209 CONFLICT
SEQADV 1BN7 GLY A 303 GB 3114657 ALA A 292 CONFLICT
SEQADV 1BN7 ALA A 305 GB 3114657 CONFLICT
SEQRES 1 A 294 MET SER GLU ILE GLY THR GLY PHE PRO PHE ASP PRO HIS
SEQRES 2 A 294 TYR VAL GLU VAL LEU GLY GLU ARG MET HIS TYR VAL ASP
SEQRES 3 A 294 VAL GLY PRO ARG ASP GLY THR PRO VAL LEU PHE LEU HIS
SEQRES 4 A 294 GLY ASN PRO THR SER SER TYR LEU TRP ARG ASN ILE ILE
SEQRES 5 A 294 PRO HIS VAL ALA PRO SER HIS ARG CYS ILE ALA PRO ASP
SEQRES 6 A 294 LEU ILE GLY MET GLY LYS SER ASP LYS PRO ASP LEU ASP
SEQRES 7 A 294 TYR PHE PHE ASP ASP HIS VAL ARG TYR LEU ASP ALA PHE
SEQRES 8 A 294 ILE GLU ALA LEU GLY LEU GLU GLU VAL VAL LEU VAL ILE
SEQRES 9 A 294 HIS ASP TRP GLY SER ALA LEU GLY PHE HIS TRP ALA LYS
SEQRES 10 A 294 ARG ASN PRO GLU ARG VAL LYS GLY ILE ALA CYS MET GLU
SEQRES 11 A 294 PHE ILE ARG PRO ILE PRO THR TRP ASP GLU TRP PRO GLU
SEQRES 12 A 294 PHE ALA ARG GLU THR PHE GLN ALA PHE ARG THR ALA ASP
SEQRES 13 A 294 VAL GLY ARG GLU LEU ILE ILE ASP GLN ASN ALA PHE ILE
SEQRES 14 A 294 GLU GLY VAL LEU PRO LYS CYS VAL VAL ARG PRO LEU THR
SEQRES 15 A 294 GLU VAL GLU MET ASP HIS TYR ARG GLU PRO PHE LEU LYS
SEQRES 16 A 294 PRO VAL ASP ARG GLU PRO LEU TRP ARG PHE PRO ASN GLU
SEQRES 17 A 294 ILE PRO ILE ALA GLY GLU PRO ALA ASN ILE VAL ALA LEU
SEQRES 18 A 294 VAL GLU ALA TYR MET ASN TRP LEU HIS GLN SER PRO VAL
SEQRES 19 A 294 PRO LYS LEU LEU PHE TRP GLY THR PRO GLY VAL LEU ILE
SEQRES 20 A 294 PRO PRO ALA GLU ALA ALA ARG LEU ALA GLU SER LEU PRO
SEQRES 21 A 294 ASN CYS LYS THR VAL ASP ILE GLY PRO GLY LEU HIS TYR
SEQRES 22 A 294 LEU GLN GLU ASP ASN PRO ASP LEU ILE GLY SER GLU ILE
SEQRES 23 A 294 ALA ARG TRP LEU PRO GLY LEU ALA
HET ACT 320 4
HETNAM ACT ACETATE ION
FORMUL 2 ACT C2 H3 O2 1-
FORMUL 3 HOH *369(H2 O1)
HELIX 1 1 SER A 56 VAL A 66 5 11
HELIX 2 2 PHE A 92 ALA A 105 1 14
HELIX 3 3 ASP A 117 ARG A 129 1 13
HELIX 4 4 PRO A 131 ARG A 133 5 3
HELIX 5 5 TRP A 149 GLU A 151 5 3
HELIX 6 6 GLU A 154 PHE A 163 1 10
HELIX 7 7 VAL A 168 ILE A 173 1 6
HELIX 8 8 ALA A 178 GLU A 181 1 4
HELIX 9 9 VAL A 183 CYS A 187 1 5
HELIX 10 10 GLU A 194 PHE A 204 1 11
HELIX 11 11 PRO A 207 GLU A 219 5 13
HELIX 12 12 ALA A 227 GLN A 242 1 16
HELIX 13 13 PRO A 260 SER A 269 1 10
HELIX 14 14 LEU A 285 ASP A 288 1 4
HELIX 15 15 PRO A 290 LEU A 301 1 12
SHEET 1 A 3 HIS A 24 VAL A 28 0
SHEET 2 A 3 GLU A 31 VAL A 38 -1 N TYR A 35 O HIS A 24
SHEET 3 A 3 CYS A 72 PRO A 75 -1 N ALA A 74 O VAL A 36
SHEET 1 B 5 PRO A 45 LEU A 49 0
SHEET 2 B 5 VAL A 111 HIS A 116 1 N VAL A 112 O PRO A 45
SHEET 3 B 5 VAL A 134 MET A 140 1 N LYS A 135 O VAL A 111
SHEET 4 B 5 LYS A 247 TRP A 251 1 N LEU A 248 O ILE A 137
SHEET 5 B 5 CYS A 273 ASP A 277 1 N LYS A 274 O LYS A 247
CISPEP 1 ASN A 52 PRO A 53 0 -0.59
CISPEP 2 GLU A 225 PRO A 226 0 -1.03
CISPEP 3 THR A 253 PRO A 254 0 0.89
SITE 1 CAT 3 ASP A 117 GLU A 141 HIS A 283
CRYST1 93.630 79.890 42.930 90.00 90.00 90.00 P 21 21 2 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 0.010680 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012517 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023294 0.00000
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