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- PDB-1edd: CRYSTALLOGRAPHIC AND FLUORESCENCE STUDIES OF THE INTERACTION OF H... -
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Open data
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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 | ||||||
![]() | HALOALKANE DEHALOGENASE | ||||||
![]() | DEHALOGENASE | ||||||
Function / homology | ![]() 1,2-dichloroethane catabolic process / haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Verschueren, K.H.G. / Dijkstra, B.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.1 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 366.4 KB | Display | ![]() |
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Full document | ![]() | 379 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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. |
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Components
#1: Protein | Mass: 35175.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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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: ![]() |
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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 |
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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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