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- PDB-3fbw: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fbw | ||||||
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Title | Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant C176Y | ||||||
![]() | Haloalkane dehalogenase | ||||||
![]() | HYDROLASE / Detoxification / alpha/beta-Hydrolase / catalytic triad / halide-binding site | ||||||
Function / homology | ![]() haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dohnalek, J. / Stsiapanava, A. / Gavira, J.A. / Kuta Smatanova, I. / Kuty, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.7 KB | Display | ![]() |
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PDB format | ![]() | 121.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 440.9 KB | Display | ![]() |
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Full document | ![]() | 447.2 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fwhC ![]() 3g9xC ![]() 1bn6S C: citing same article ( S: Starting model for refinement |
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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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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.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-BEZ / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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