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HEADER DEHALOGENASE 18-MAY-98 1BEZ
TITLE HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR
TITLE 2 AT PH 5
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 MUTATION: I2V, W175Y;
COMPND 7 BIOLOGICAL_UNIT: MONOMER;
COMPND 8 OTHER_DETAILS: WITH ACETIC ACID
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOBACTER AUTOTROPHICUS;
SOURCE 3 STRAIN: GJ10;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI
KEYWDS DEHALOGENASE, ALPHA/BETA-HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR I.S.RIDDER,G.J.VOS,H.J.ROZEBOOM,K.H.KALK,B.W.DIJKSTRA
REVDAT 1 11-NOV-98 1BEZ 0
JRNL AUTH G.H.KROOSHOF,I.S.RIDDER,A.W.J.W.TEPPER,G.J.VOS,
JRNL AUTH 2 H.J.ROZEBOOM,K.H.KALK,B.W.DIJKSTRA,D.B.JANSSEN
JRNL TITL KINETIC ANALYSIS AND X-RAY STRUCTURE OF HALOALKANE
JRNL TITL 2 DEHALOGENASE WITH A MODIFIED HALIDE-BINDING SITE
JRNL REF BIOCHEMISTRY V. 37 15013 1998
JRNL REFN ASTM BICHAW US ISSN 0006-2960 0033
REMARK 1
REMARK 1 REFERENCE 1
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 2
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 3
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 4
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. 2.1 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) : 2.1
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.0
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0001
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 78.4
REMARK 3 NUMBER OF REFLECTIONS : 13123
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT, EXCEPT
REMARK 3 LAST STEP IN WHICH ALL DATA (WORK+TEST SET) WERE USED
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM EXTENSION OF SET
REMARK 3 USED FOR 1BEE
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.225
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0
REMARK 3 FREE R VALUE TEST SET COUNT : 686
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) : 2.10
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.5
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1381
REMARK 3 BIN R VALUE (WORKING SET) : 0.245
REMARK 3 BIN FREE R VALUE : 0.289
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.0
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67
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 : 2476
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 8
REMARK 3 SOLVENT ATOMS : 279
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 16.3
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.1
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) : 0.19
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) : 1.5
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.4
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.2
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) : 2.31 ; 1.5
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.73 ; 2.0
REMARK 3 SIDE-CHAIN BOND (A**2) : 3.30 ; 2.0
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.93 ; 2.5
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 : PARAM19.WAT
REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO
REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1BEZ COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-SEP-1995
REMARK 200 TEMPERATURE (KELVIN) : 120
REMARK 200 PH : 5.0
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 : ELLIOT GX21
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : FAST AREA DETECTOR
REMARK 200 DETECTOR MANUFACTURER : ENRAF NONIUS
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNES
REMARK 200 DATA SCALING SOFTWARE : BIOMOL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13700
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.10
REMARK 200 RESOLUTION RANGE LOW (A) : 31
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 79
REMARK 200 DATA REDUNDANCY : 4.8
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.075
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13
REMARK 200 COMPLETENESS FOR SHELL (%) : 61
REMARK 200 DATA REDUNDANCY IN SHELL : 1.4
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.137
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: PDB ENTRY 1BEE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 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 46.51595
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.15068
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.51595
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.15068
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
DBREF 1BEZ 1 310 SWS P22643 HALO_XANAU 1 310
SEQADV 1BEZ VAL 2 SWS P22643 ILE 2 CLONING ARTIFACT
SEQADV 1BEZ TYR 175 SWS P22643 TRP 175 ENGINEERED
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 CYS 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 TYR 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 CYS 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
HET ACY 401 4
HET ACY 402 4
HETNAM ACY ACETIC ACID
FORMUL 2 ACY 2(C2 H4 O2)
FORMUL 3 HOH *279(H2 O1)
HELIX 1 1 SER 60 SER 73 5 14
HELIX 2 2 PHE 99 LEU 113 1 15
HELIX 3 3 TRP 125 ALA 136 1 12
HELIX 4 4 PRO 159 THR 166 5 8
HELIX 5 5 GLY 171 THR 181 1 11
HELIX 6 6 LEU 187 TRP 194 1 8
HELIX 7 7 GLU 200 ALA 208 1 9
HELIX 8 8 ALA 217 ALA 227 1 11
HELIX 9 9 GLN 231 ASP 247 1 17
HELIX 10 10 GLY 264 LEU 274 1 11
HELIX 11 11 VAL 291 GLU 308 5 18
SHEET 1 S1 2 ASN 3 ILE 5 0
SHEET 2 S1 2 LYS 90 VAL 92 -1
SHEET 1 S2 8 ASN 23 LEU 25 0
SHEET 2 S2 8 ALA 36 GLU 41 -1
SHEET 3 S2 8 ARG 76 ASP 81 -1
SHEET 4 S2 8 ASP 48 LEU 53 1
SHEET 5 S2 8 ILE 118 VAL 122 1
SHEET 6 S2 8 PHE 141 MET 147 1
SHEET 7 S2 8 GLN 251 GLY 257 1
SHEET 8 S2 8 LEU 282 ILE 284 1
CISPEP 1 GLU 56 PRO 57 0 0.10
CISPEP 2 GLN 167 PRO 168 0 0.10
CRYST1 93.030 72.300 40.960 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 0.010749 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013831 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024414 0.00000 |