+Open data
-Basic information
Entry | Database: PDB / ID: 1hde | ||||||
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Title | HALOALKANE DEHALOGENASE MUTANT WITH PHE 172 REPLACED WITH TRP | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
Keywords | DEHALOGENASE / HYDROLASE / DETOXIFICATION | ||||||
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: 2.7 Å | ||||||
Authors | Ridder, I.S. / Kalk, K.H. / Dijkstra, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Kinetic characterization and X-ray structure of a mutant of haloalkane dehalogenase with higher catalytic activity and modified substrate range. Authors: Schanstra, J.P. / Ridder, I.S. / Heimeriks, G.J. / Rink, R. / Poelarends, G.J. / Kalk, K.H. / Dijkstra, B.W. / Janssen, D.B. #1: 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. #2: 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. #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 | 1hde.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hde.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hde ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hde | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.997561, -0.056672, 0.040741), Vector: |
-Components
#1: Protein | Mass: 35214.832 Da / Num. of mol.: 2 / Mutation: F172W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / Strain: GJ10 / Cell line: BL21 / Plasmid: PGELAF+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P22643, haloalkane dehalogenase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40 % | |||||||||||||||
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Crystal grow | pH: 5.8 / Details: pH 5.8 | |||||||||||||||
Crystal | *PLUS | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 15796 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.101 |
Reflection | *PLUS Highest resolution: 2.67 Å / Lowest resolution: 35 Å / Num. measured all: 43099 |
Reflection shell | *PLUS Highest resolution: 2.67 Å / Lowest resolution: 2.77 Å / % possible obs: 83.1 % / Rmerge(I) obs: 0.312 |
-Processing
Software |
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Refinement | Resolution: 2.7→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 13.15 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||
Refine LS restraints | *PLUS
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