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Yorodumi- PDB-1edd: CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1edd | ||||||
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Title | CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF HALOALKANE DEHALOGENASE WITH HALIDE IONS: STUDIES WITH HALIDE COMPOUNDS REVEAL A HALIDE BINDING SITE IN THE ACTIVE SITE | ||||||
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: 2.19 Å | ||||||
Authors | Verschueren, K.H.G. / Dijkstra, B.W. | ||||||
Citation | Journal: Biochemistry / Year: 1993 Title: Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site. Authors: Verschueren, K.H. / Kingma, J. / Rozeboom, H.J. / Kalk, K.H. / Janssen, D.B. / 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1edd.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1edd.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 1edd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1edd_validation.pdf.gz | 366.4 KB | Display | wwPDB validaton report |
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Full document | 1edd_full_validation.pdf.gz | 379 KB | Display | |
Data in XML | 1edd_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1edd_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1edd ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1edd | HTTPS FTP |
-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: RESIDUES 57 AND 168 ARE CIS PROLINES. |
-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-CL / |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE DEHALOGENASE HAS BEEN SOAKED IN 10 MM SODIUM CHLORIDE. THE CHLORIDE ION WAS FOUND IN THE ACTIVE ...THE DEHALOGENA |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.73 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 200.611-612 / PH range low: 7.2 / PH range high: 5.4 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.19 Å / Lowest resolution: 9999 Å / Num. obs: 12376 / % possible obs: 81.2 % / Num. measured all: 34777 / Rmerge(I) obs: 0.0611 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.19→15 Å / σ(F): 3 /
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Refinement step | Cycle: LAST / Resolution: 2.19→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.19 Å / Lowest resolution: 15 Å / Num. reflection obs: 12376 / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.3 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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