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Yorodumi- PDB-3fbw: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fbw | ||||||
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Title | Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant C176Y | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / Detoxification / alpha/beta-Hydrolase / catalytic triad / halide-binding site | ||||||
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: 1.23 Å | ||||||
Authors | Dohnalek, J. / Stsiapanava, A. / Gavira, J.A. / Kuta Smatanova, I. / Kuty, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels. Authors: Stsiapanava, A. / Dohnalek, J. / Gavira, J.A. / Kuty, M. / Koudelakova, T. / Damborsky, J. / Kuta Smatanova, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fbw.cif.gz | 157.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fbw.ent.gz | 121.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/3fbw ftp://data.pdbj.org/pub/pdb/validation_reports/fb/3fbw | HTTPS FTP |
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-Related structure data
Related structure data | 3fwhC 3g9xC 1bn6S C: citing same article (ref.) 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: 34170.898 Da / Num. of mol.: 1 / Mutation: C176Y Source method: isolated from a genetically manipulated source Details: The active site partially occupied by a small ligand and by a chloride ion Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Strain: NCIMB 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-BEZ / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.54 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.08M bicine, 8% PEG 8000, 0.08M magnesium chloride, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8158 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 16, 2007 |
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8158 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→100 Å / Num. all: 88814 / Num. obs: 88814 / % possible obs: 100 % / Observed criterion σ(I): -999 / Redundancy: 7.4 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 1.23→1.25 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4384 / Rsym value: 0.581 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BN6 Resolution: 1.23→100 Å / Num. parameters: 26510 / Num. restraintsaints: 37060 Isotropic thermal model: MIXED ISOTROPIC AND ANISOTROPIC THERMAL MODEL Cross valid method: FREE R / σ(F): 0 Stereochemistry target values: ENGH & HUBER, LIGAND TARGET VALUES BASED ON AVERAGED BEST CAMBRIDGE STRUCTURAL DATABASE VALUES Details: CONJUGATE GRADIENT LEAST SQUARES REFINEMENT IN SHELXL97 WITH ANISOTROPIC ADPS FOR ALL ATOMS EXCEPT FOR WATER MOLECULES ABOVE A CERTAIN ADP CUTTOF
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Solvent computation | Solvent model: BABINET, SHELXL97 IMPLEMENTATION, G=1.007, U=4.133 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.4 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.122 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 61 / Occupancy sum hydrogen: 2267.9 / Occupancy sum non hydrogen: 2738.52 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→100 Å
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Refine LS restraints |
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