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HEADER HYDROLASE 14-JAN-99 1B6G
TITLE HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING CHLORIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HALOALKANE DEHALOGENASE;
COMPND 3 CHAIN: NULL;
COMPND 4 EC: 3.8.1.5;
COMPND 5 ENGINEERED: YES;
COMPND 6 BIOLOGICAL_UNIT: MONOMER
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOBACTER AUTOTROPHICUS;
SOURCE 3 STRAIN: GJ10;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI
KEYWDS HYDROLASE, HALOALKANE DEHALOGENASE, ALPHA/BETA-HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR I.S.RIDDER,H.J.ROZEBOOM,B.W.DIJKSTRA
REVDAT 1 13-JUL-99 1B6G 0
JRNL AUTH I.S.RIDDER,H.J.ROZEBOOM,B.W.DIJKSTRA
JRNL TITL HALOALKANE DEHALOGENASE FROM XANTHOBACTER
JRNL TITL 2 AUTOTROPHICUS GJ10 REFINED AT 1.15 A
JRNL REF ACTA CRYSTALLOGR., SECT.D V. 55 1273 1999
JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449 0766
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH G.H.KROOSHOF,I.S.RIDDER,A.W.TEPPER,G.J.VOS,
REMARK 1 AUTH 2 H.J.ROZEBOOM,K.H.KALK,B.W.DIJKSTRA,D.B.JANSSEN
REMARK 1 TITL KINETIC ANALYSIS AND X-RAY STRUCTURE OF HALOALKANE
REMARK 1 TITL 2 DEHALOGENASE WITH A MODIFIED HALIDE-BINDING SITE
REMARK 1 REF BIOCHEMISTRY V. 37 15013 1998
REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 0033
REMARK 1 REFERENCE 2
REMARK 1 AUTH K.H.VERSCHUEREN,F.SELJEE,H.J.ROZEBOOM,K.H.KALK,
REMARK 1 AUTH 2 B.W.DIJKSTRA
REMARK 1 TITL CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC
REMARK 1 TITL 2 MECHANISM OF HALOALKANE DEHALOGENASE
REMARK 1 REF NATURE V. 363 693 1993
REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 0006
REMARK 1 REFERENCE 3
REMARK 1 AUTH K.H.VERSCHUEREN,S.M.FRANKEN,H.J.ROZEBOOM,K.H.KALK,
REMARK 1 AUTH 2 B.W.DIJKSTRA
REMARK 1 TITL REFINED X-RAY STRUCTURES OF HALOALKANE DEHALOGENASE
REMARK 1 TITL 2 AT PH 6.2 AND PH 8.2 AND IMPLICATIONS FOR THE
REMARK 1 TITL 3 REACTION MECHANISM
REMARK 1 REF J.MOL.BIOL. V. 232 856 1993
REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 0070
REMARK 1 REFERENCE 4
REMARK 1 AUTH S.M.FRANKEN,H.J.ROZEBOOM,K.H.KALK,B.W.DIJKSTRA
REMARK 1 TITL CRYSTAL STRUCTURE OF HALOALKANE DEHALOGENASE: AN
REMARK 1 TITL 2 ENZYME TO DETOXIFY HALOGENATED ALKANES
REMARK 1 REF EMBO J. V. 10 1297 1991
REMARK 1 REFN ASTM EMJODG UK ISSN 0261-4189 0897
REMARK 1 REFERENCE 5
REMARK 1 AUTH H.J.ROZEBOOM,J.KINGMA,D.B.JANSSEN,B.W.DIJKSTRA
REMARK 1 TITL CRYSTALLIZATION OF HALOALKANE DEHALOGENASE FROM
REMARK 1 TITL 2 XANTHOBACTER AUTOTROPHICUS GJ10
REMARK 1 REF J.MOL.BIOL. V. 200 611 1988
REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 0070
REMARK 2
REMARK 2 RESOLUTION. 1.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 CROSS-VALIDATION METHOD : FREE R
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1051
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1059
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.1454
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.5
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5193
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 94752
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.0972
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.0981
REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.1368
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.5
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 4419
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 80648
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2625
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 63
REMARK 3 SOLVENT ATOMS : 601
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3064.82
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2406.85
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 34
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 29678
REMARK 3 NUMBER OF RESTRAINTS : 36636
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.013
REMARK 3 ANGLE DISTANCES (A) : 0.029
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.0281
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.092
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.105
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.121
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.042
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.080
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED
REMARK 3 RWORK (NO CUTOFF) FROM 16.4% TO 13.4% AND RFREE FROM 19.6%
REMARK 3 TO 17.3%.
REMARK 4
REMARK 4 1B6G COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 6
REMARK 6 THE FOLLOWING ARE APPARENT CLOSE CONTACTS BUT ACTUALLY
REMARK 6 INVOLVE DIFFERENT ALTERNATE CONFORMATIONS:
REMARK 6 CLOSE CONTACT C3 GOL 1204 - O HOH 2608 0.604
REMARK 6 CLOSE CONTACT CD AGLU 280 - O HOH 2586 0.938
REMARK 6 CLOSE CONTACT CE BLYS 192 - O HOH 2549 0.662
REMARK 6 CLOSE CONTACT NH1BARG 300 - O HOH 2607 1.006
REMARK 6 CLOSE CONTACT NZ BLYS 192 - O HOH 2549 0.874
REMARK 6 CLOSE CONTACT O HOH 2558 - O HOH 2565 1.168
REMARK 6 CLOSE CONTACT O HOH 2565 - O HOH 2558 1.168
REMARK 6 CLOSE CONTACT OD1BASP 137 - O HOH 2585 0.681
REMARK 6 CLOSE CONTACT OD2BASP 137 - O HOH 2584 0.868
REMARK 6 CLOSE CONTACT OE1AGLU 280 - O HOH 2586 0.955
REMARK 6 CLOSE CONTACT OE1BGLU 72 - O HOH 2591 1.117
REMARK 6 CLOSE CONTACTCL CL 1999 - O HOH 2000 0.267
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 06-APR-1998
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-EH3
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9475
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MAR
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94837
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.152
REMARK 200 RESOLUTION RANGE LOW (A) : 30.0
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NONE
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 200 DATA REDUNDANCY : 3.67
REMARK 200 R MERGE (I) : 0.039
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 30.8
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17
REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5
REMARK 200 DATA REDUNDANCY IN SHELL : 3.52
REMARK 200 R MERGE FOR SHELL (I) : 0.316
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : 2.7
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR
REMARK 200 REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: 1BE0
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS:
REMARK 280 PROTEIN WAS CRYSTALLIZED FROM
REMARK 280 50% AMMONIUM SULFATE, 100 MM MES, PH 5.6
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 46.09145
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.01527
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.09145
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.01527
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 O HOH 2499
REMARK 375
REMARK 375 REMARK: NULL
REMARK 600 IDENTITY OF THE ION IN THE CSB RESIDUE WAS DETERMINED FROM
REMARK 600 ANOMALOUS SIGNAL, IN COMBINATION WITH
REMARK 600 ELEMENTAL ANALYSIS OF THE SOAKING SOLUTION
REMARK 600
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: ACT
REMARK 800 SITE_DESCRIPTION:
REMARK 800 CATALYTIC TRIAD RESIDUES
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 DISCREPANCY AT 2 IS DUE TO EXPRESSION SYSTEM
DBREF 1B6G 1 310 SWS P22643 HALO_XANAU 1 310
SEQADV 1B6G VAL 2 SWS P22643 ILE 2 CLONING ARTIFACT
SEQADV 1B6G CSB 150 SWS P22643 CYS 150 MODIFIED RESIDUE
SEQADV 1B6G CSB 233 SWS P22643 CYS 233 MODIFIED RESIDUE
SEQRES 1 310 MET VAL ASN ALA ILE ARG THR PRO ASP GLN ARG PHE SER
SEQRES 2 310 ASN LEU ASP GLN TYR PRO PHE SER PRO ASN TYR LEU ASP
SEQRES 3 310 ASP LEU PRO GLY TYR PRO GLY LEU ARG ALA HIS TYR LEU
SEQRES 4 310 ASP GLU GLY ASN SER ASP ALA GLU ASP VAL PHE LEU CYS
SEQRES 5 310 LEU HIS GLY GLU PRO THR TRP SER TYR LEU TYR ARG LYS
SEQRES 6 310 MET ILE PRO VAL PHE ALA GLU SER GLY ALA ARG VAL ILE
SEQRES 7 310 ALA PRO ASP PHE PHE GLY PHE GLY LYS SER ASP LYS PRO
SEQRES 8 310 VAL ASP GLU GLU ASP TYR THR PHE GLU PHE HIS ARG ASN
SEQRES 9 310 PHE LEU LEU ALA LEU ILE GLU ARG LEU ASP LEU ARG ASN
SEQRES 10 310 ILE THR LEU VAL VAL GLN ASP TRP GLY GLY PHE LEU GLY
SEQRES 11 310 LEU THR LEU PRO MET ALA ASP PRO SER ARG PHE LYS ARG
SEQRES 12 310 LEU ILE ILE MET ASN ALA CSB LEU MET THR ASP PRO VAL
SEQRES 13 310 THR GLN PRO ALA PHE SER ALA PHE VAL THR GLN PRO ALA
SEQRES 14 310 ASP GLY PHE THR ALA TRP LYS TYR ASP LEU VAL THR PRO
SEQRES 15 310 SER ASP LEU ARG LEU ASP GLN PHE MET LYS ARG TRP ALA
SEQRES 16 310 PRO THR LEU THR GLU ALA GLU ALA SER ALA TYR ALA ALA
SEQRES 17 310 PRO PHE PRO ASP THR SER TYR GLN ALA GLY VAL ARG LYS
SEQRES 18 310 PHE PRO LYS MET VAL ALA GLN ARG ASP GLN ALA CSB ILE
SEQRES 19 310 ASP ILE SER THR GLU ALA ILE SER PHE TRP GLN ASN ASP
SEQRES 20 310 TRP ASN GLY GLN THR PHE MET ALA ILE GLY MET LYS ASP
SEQRES 21 310 LYS LEU LEU GLY PRO ASP VAL MET TYR PRO MET LYS ALA
SEQRES 22 310 LEU ILE ASN GLY CYS PRO GLU PRO LEU GLU ILE ALA ASP
SEQRES 23 310 ALA GLY HIS PHE VAL GLN GLU PHE GLY GLU GLN VAL ALA
SEQRES 24 310 ARG GLU ALA LEU LYS HIS PHE ALA GLU THR GLU
MODRES 1B6G CSB 150 CYS LEAD BOUND TO SG
MODRES 1B6G CSB 233 CYS LEAD BOUND TO SG
HET CSB 150 7
HET CSB 233 7
HET SO4 1101 5
HET GOL 1201 6
HET GOL 1202 6
HET GOL 1203 6
HET GOL 1204 6
HET GOL 1205 6
HET GOL 1206 6
HET GOL 1207 6
HET CL 1998 1
HET CL 1999 1
HETNAM CSB CYS BOUND TO LEAD ION
HETNAM SO4 SULFATE ION
HETNAM GOL GLYCEROL
HETNAM CL CHLORIDE ION
FORMUL 1 CSB 2(C3 H6 N1 O2 PB1 S1 1+)
FORMUL 2 SO4 O4 S1 2-
FORMUL 3 GOL 7(C3 H8 O3)
FORMUL 4 CL 2(CL1 1-)
FORMUL 5 HOH *601(H2 O1)
HELIX 1 1 ASP 9 PHE 12 5 4
HELIX 2 2 SER 60 SER 73 5 14
HELIX 3 3 GLU 94 ASP 96 5 3
HELIX 4 4 PHE 99 LEU 113 1 15
HELIX 5 5 ASP 124 THR 132 1 9
HELIX 6 6 PRO 134 ALA 136 5 3
HELIX 7 7 PRO 138 ARG 140 5 3
HELIX 8 8 PRO 159 VAL 165 5 7
HELIX 9 9 PHE 172 VAL 180 1 9
HELIX 10 10 LEU 187 TRP 194 1 8
HELIX 11 11 GLU 200 ALA 207 1 8
HELIX 12 12 THR 213 TYR 215 5 3
HELIX 13 13 ALA 217 ALA 227 1 11
HELIX 14 14 GLN 231 ASN 246 5 16
HELIX 15 15 PRO 265 LEU 274 1 10
HELIX 16 16 VAL 291 GLU 308 5 18
SHEET 1 A 8 ASN 23 ASP 26 0
SHEET 2 A 8 ARG 35 GLY 42 -1 N TYR 38 O ASN 23
SHEET 3 A 8 ARG 76 PRO 80 -1 N ALA 79 O LEU 39
SHEET 4 A 8 VAL 49 CYS 52 1 N PHE 50 O ARG 76
SHEET 5 A 8 ILE 118 VAL 122 1 N THR 119 O VAL 49
SHEET 6 A 8 PHE 141 MET 147 1 N LYS 142 O ILE 118
SHEET 7 A 8 GLN 251 GLY 257 1 N GLN 251 O LEU 144
SHEET 8 A 8 LEU 282 ILE 284 1 N LEU 282 O ILE 256
LINK N CSB 150 C ALA 149
LINK C CSB 150 N LEU 151
LINK N CSB 233 C ALA 232
LINK C CSB 233 N ILE 234
CISPEP 1 GLU 56 PRO 57 0 -20.30
CISPEP 2 GLN 167 PRO 168 0 -5.39
SITE 1 ACT 3 ASP 124 HIS 289 ASP 260
CRYST1 92.180 72.029 40.909 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 0.010848 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013883 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024444 0.00000 |