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Yorodumi- PDB-4k2a: Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizo... -
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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 | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / Structural Genomics / Enzyme Function Initiative / Structure 2 Function Project / S2F / two domain organization / dimer catalytic pentad / halogen binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bradyrhizobium elkanii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k2a.cif.gz | 467 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k2a.ent.gz | 389.2 KB | Display | PDB format |
PDBx/mmJSON format | 4k2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k2a_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 4k2a_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 4k2a_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 4k2a_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k2a ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k2a | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-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.) Bradyrhizobium elkanii (bacteria) / Strain: USDA94 / Gene: dbeA, dhaA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E2RV62, haloalkane dehalogenase #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
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: 0.918 Å / Relative weight: 1 |
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 |
-Processing
Software |
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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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