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- PDB-3sk0: structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sk0 | ||||||
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Title | structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant DhaA12 | ||||||
![]() | Haloalkane dehalogenase | ||||||
![]() | HYDROLASE / catalytic pentad / alpha/beta-Hydrolase Fold / halide binding / hydrolytic dehalogenation | ||||||
Function / homology | ![]() haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lahoda, M. / Stsiapanava, A. / Mesters, J. / Koudelakova, T. / Damborsky, J. / Kuta-Smatanova, I. | ||||||
![]() | ![]() Title: Dynamics and hydration explain failed functional transformation in dehalogenase design. Authors: Sykora, J. / Brezovsky, J. / Koudelakova, T. / Lahoda, M. / Fortova, A. / Chernovets, T. / Chaloupkova, R. / Stepankova, V. / Prokop, Z. / Smatanova, I.K. / Hof, M. / Damborsky, J. #1: ![]() Title: Crystal structure of haloalkane dehalogenase mutant DhaA12 from Gram-positive bacterium Rhodococcus rhodochrous NCIMB13064 Authors: Lahoda, M. / Koudelakova, T. / Stsiapanava, A. / Mesters, J. / 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 | ![]() | 82.9 KB | Display | ![]() |
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PDB format | ![]() | 60.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.4 KB | Display | ![]() |
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Full document | ![]() | 425.1 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3fbwS 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: 35397.043 Da / Num. of mol.: 1 Mutation: W138F, 139HHTEVAEEQDH149 insertion, P150A, F152A, G179R, A180V, K183G, C184G, V253A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 100 mM MES sodium salt, 20% peg 4000, pH 6.1, 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: Nov 24, 2009 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→10 Å / Num. obs: 34658 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4241 / Rsym value: 0.37 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3FBW Resolution: 1.78→10 Å / Num. parameters: 11235 / Num. restraintsaints: 10651 / Isotropic thermal model: isotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: CONJUGATE GRADIENT LEAST SQUARES REFINEMENT IN SHELXL 97
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Displacement parameters | Biso mean: 17.1 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.188 Å / Luzzati d res low obs: 6.67 Å / Num. disordered residues: 15 / Occupancy sum hydrogen: 2288 / Occupancy sum non hydrogen: 2751 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.88 Å
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