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Yorodumi- PDB-3sk0: structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sk0 | ||||||
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Title | structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA mutant DhaA12 | ||||||
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: 1.78 Å | ||||||
Authors | Lahoda, M. / Stsiapanava, A. / Mesters, J. / Koudelakova, T. / Damborsky, J. / Kuta-Smatanova, I. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 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: Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sk0.cif.gz | 82.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sk0.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 3sk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sk/3sk0 ftp://data.pdbj.org/pub/pdb/validation_reports/sk/3sk0 | 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: 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.) Rhodococcus rhodochrous (bacteria) / 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-CL / |
#3: 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: 2.11 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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