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- PDB-1bez: HALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5 -

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Basic information

Entry
Database: PDB / ID: 1bez
TitleHALOALKANE DEHALOGENASE MUTANT WITH TRP 175 REPLACED BY TYR AT PH 5
ComponentsHALOALKANE DEHALOGENASE
KeywordsDEHALOGENASE / ALPHA/BETA-HYDROLASE
Function / homology
Function and homology information


1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / epoxide hydrolase activity / response to toxic substance
Similarity search - Function
Haloalkane dehalogenase, subfamily 1 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Haloalkane dehalogenase
Similarity search - Component
Biological speciesXanthobacter autotrophicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsRidder, I.S. / Vos, G.J. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1998
Title: Kinetic analysis and X-ray structure of haloalkane dehalogenase with a modified halide-binding site.
Authors: Krooshof, G.H. / Ridder, I.S. / Tepper, A.W. / Vos, G.J. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. / Janssen, D.B.
#1: Journal: Nature / Year: 1993
Title: Crystallographic Analysis of the Catalytic Mechanism of Haloalkane Dehalogenase
Authors: Verschueren, K.H. / Seljee, F. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined X-Ray Structures of Haloalkane Dehalogenase at Ph 6.2 And Ph 8.2 And Implications for the Reaction Mechanism
Authors: Verschueren, K.H. / Franken, S.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#3: Journal: Embo J. / Year: 1991
Title: Crystal Structure of Haloalkane Dehalogenase: An Enzyme to Detoxify Halogenated Alkanes
Authors: Franken, S.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of Haloalkane Dehalogenase from Xanthobacter Autotrophicus Gj10
Authors: Rozeboom, H.J. / Kingma, J. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionMay 18, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HALOALKANE DEHALOGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2593
Polymers35,1391
Non-polymers1202
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.030, 72.300, 40.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HALOALKANE DEHALOGENASE


Mass: 35138.734 Da / Num. of mol.: 1 / Mutation: I2V, W175Y
Source method: isolated from a genetically manipulated source
Details: WITH ACETIC ACID / Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Production host: Escherichia coli (E. coli) / References: UniProt: P22643, haloalkane dehalogenase
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 38 %
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM 50% AMMONIUM SULFATE, 100 MM MES, PH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
2100 mMMES1drop
350 %ammonium sulfate1reservoir
4100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 11, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→31 Å / Num. obs: 13700 / % possible obs: 79 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.075 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 1.4 % / Rsym value: 0.137 / % possible all: 61
Reflection
*PLUS
Num. measured all: 65239 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 60.5 % / Rmerge(I) obs: 0.136

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
MADNESdata reduction
BIOMOLdata scaling
X-PLOR3.843phasing
RefinementStarting model: PDB ENTRY 1BEE

1bee


Resolution: 2.1→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.0001
Cross valid method: THROUGHOUT, EXCEPT LAST STEP IN WHICH ALL DATA (WORK+TEST SET) WERE USED
σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 686 5 %RANDOM EXTENSION OF SET USED FOR 1BEE
Rwork0.171 ---
obs0.171 13123 78.4 %-
Displacement parametersBiso mean: 14.1 Å2
Refine analyzeLuzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 8 279 2763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.311.5
X-RAY DIFFRACTIONx_mcangle_it3.732
X-RAY DIFFRACTIONx_scbond_it3.32
X-RAY DIFFRACTIONx_scangle_it4.932.5
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.289 67 5 %
Rwork0.245 1381 -
obs--67.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.WATTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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