+Open data
-Basic information
Entry | Database: PDB / ID: 1be0 | ||||||
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Title | HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING ACETIC ACID | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
Keywords | DEHALOGENASE / ALPHA/BETA-HYDROLASE | ||||||
Function / homology | Function and homology information 1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Xanthobacter autotrophicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.96 Å | ||||||
Authors | Ridder, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1be0.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1be0.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 1be0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1be0_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 1be0_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 1be0_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1be0_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/1be0 ftp://data.pdbj.org/pub/pdb/validation_reports/be/1be0 | HTTPS FTP |
-Related structure data
Related structure data | 1beeSC 1bezC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35161.770 Da / Num. of mol.: 1 / Mutation: I2V Source method: isolated from a genetically manipulated source Details: ACETIC ACID / Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Production host: Escherichia coli (E. coli) / References: UniProt: P22643, haloalkane dehalogenase |
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#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-ACY / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37 % | |||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 8, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→31 Å / Num. obs: 18082 / % possible obs: 87.2 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.96→2 Å / Redundancy: 1.2 % / Rsym value: 0.181 / % possible all: 42 |
Reflection | *PLUS Num. measured all: 56912 / Rmerge(I) obs: 0.073 |
Reflection shell | *PLUS % possible obs: 42.3 % / Rmerge(I) obs: 0.191 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1BEE Resolution: 1.96→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
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Displacement parameters | Biso mean: 11.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.04 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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