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- PDB-4k2a: Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k2a | ||||||
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Title | Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94 | ||||||
![]() | Haloalkane dehalogenase![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Prudnikova, T. / Chaloupkova, R. / Rezacova, P. / Mozga, T. / Koudelakova, T. / Sato, Y. / Kuty, M. / Nagata, Y. / Damborsky, J. / Kuta Smatanova, I. / Structure 2 Function Project (S2F) | ||||||
![]() | ![]() Title: Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites. Authors: Chaloupkova, R. / Prudnikova, T. / Rezacova, P. / Prokop, Z. / Koudelakova, T. / Daniel, L. / Brezovsky, J. / Ikeda-Ohtsubo, W. / Sato, Y. / Kuty, M. / Nagata, Y. / Kuta Smatanova, I. / Damborsky, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 462.8 KB | Display | ![]() |
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PDB format | ![]() | 399.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 324 KB | Display | ![]() |
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Full document | ![]() | 330.9 KB | Display | |
Data in XML | ![]() | 51.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | ![]() Mass: 32721.256 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM Tris HCl, 20% (w/v) PEG 3350 or 4000 and 150 mM calcium acetate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2008 / Details: mirrors |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→29.71 Å / Num. all: 79384 / Num. obs: 73280 / % possible obs: 92.31 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.64 |
Reflection shell | Resolution: 2.201→2.258 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.3 / % possible all: 62.8 |
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Processing
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Refinement | Resolution: 2.2→29.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.561 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.694 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.7 Å
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Refine LS restraints |
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