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Yorodumi- PDB-4e46: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+46 | ||||||
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Title | Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / catalytic pentad / alpha/beta hydrolase fold / halide binding / hydrolytic dehalogenation | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus rhodochrous (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Stsiapanava, A. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents. Authors: Stepankova, V. / Khabiri, M. / Brezovsky, J. / Pavelka, A. / Sykora, J. / Amaro, M. / Minofar, B. / Prokop, Z. / Hof, M. / Ettrich, R. / Chaloupkova, R. / Damborsky, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e46.cif.gz | 147.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e46.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 4e46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/4e46 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/4e46 | HTTPS FTP |
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-Related structure data
Related structure data | 3fbwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33696.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Strain: NCIB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G2, haloalkane dehalogenase | ||||
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#2: Chemical | ChemComp-IPA / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium acetate, 24% PEG4000, 11% 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2009 |
Radiation | Monochromator: double crystal Si(111), horizontally focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→50 Å / Num. all: 69524 / Num. obs: 65492 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.26→1.31 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.8 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FBW Resolution: 1.26→10 Å / Num. parameters: 24815 / Num. restraintsaints: 30840 Isotropic thermal model: MIXED ISOTROPIC AND ANISOTROPIC THERMAL MODEL σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.150 FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (3476 TOTAL). FINAL ...Details: STRUCTURE SOLUTION AND REFINEMENT WERE PERFORMED USING FREE R FOR CROSS-VALIDATION THROUGHOUT: FREE R = 0.150 FROM A RANDOM TEST SET COMPRISING 5% OF REFLECTIONS (3476 TOTAL). FINAL REFINEMENT WAS PERFORMED USING ALL REFLECTIONS.
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Displacement parameters | Biso mean: 16 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 49 / Occupancy sum hydrogen: 2134 / Occupancy sum non hydrogen: 2902.45 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→10 Å
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Refine LS restraints |
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