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Yorodumi- PDB-2dhc: CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dhc | ||||||
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Title | CRYSTALLOGRAPHIC ANALYSIS OF THE CATALYTIC MECHANISM OF HALOALKANE DEHALOGENASE | ||||||
Components | HALOALKANE DEHALOGENASE | ||||||
Keywords | DEHALOGENASE | ||||||
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: 2.3 Å | ||||||
Authors | Verschueren, K.H.G. / Dijkstra, B.W. | ||||||
Citation | 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. #1: 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. #2: 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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Remark 700 | SHEET THE HELIX AND SHEET STRUCTURES ARE SIMILAR TO THOSE IN PROTEIN DATA BANK ENTRY 2HAD. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dhc.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dhc.ent.gz | 56 KB | Display | PDB format |
PDBx/mmJSON format | 2dhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/2dhc ftp://data.pdbj.org/pub/pdb/validation_reports/dh/2dhc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO 57 / 2: CIS PROLINE - PRO 168 |
-Components
#1: Protein | Mass: 35175.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthobacter autotrophicus (bacteria) / References: UniProt: P22643, haloalkane dehalogenase |
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#2: Chemical | ChemComp-DCE / |
#3: Water | ChemComp-HOH / |
Sequence details | SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.6 % | ||||||||||||||||||
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Crystal grow | *PLUS Temperature: 0 K / pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.39 Å / Num. obs: 11326 / % possible obs: 94.6 % / Num. measured all: 34590 / Rmerge(I) obs: 0.1244 |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→15 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 / Highest resolution: 2.39 Å | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_d |