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Yorodumi- PDB-3rk4: Structure of Rhodococcus rhodochrous haloalkane dehalogenase muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rk4 | ||||||
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Title | Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31 | ||||||
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: 1.31 Å | ||||||
Authors | Lahoda, M. / Stsiapanava, A. / Mesters, J. / Chaloupkova, R. / Damborsky, J. / Kuta Smatanova, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31. Authors: Lahoda, M. / Mesters, J.R. / Stsiapanava, A. / Chaloupkova, R. / Kuty, M. / 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 | 3rk4.cif.gz | 140.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rk4.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/3rk4 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/3rk4 | HTTPS FTP |
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-Related structure data
Related structure data | 4fwbC 4hzgC 3fbwS S: Starting model for refinement C: citing same article (ref.) |
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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: 34236.957 Da / Num. of mol.: 1 / Mutation: I135F, C176Y, V245F, L246I, Y273F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Strain: NCIB 13064 / Gene: dhaA, DhaA31 / 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: 2.1 Å3/Da / Density % sol: 41.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 100 mM MES Sodium salt, 29% PEG 4000, pH 6.4, 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: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→50 Å / Num. all: 314144 / Num. obs: 297181 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 1.31→1.35 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 18.3 / Rsym value: 0.081 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FBW Resolution: 1.31→10 Å / Num. parameters: 23768 / Num. restraintsaints: 29361 Isotropic thermal model: Mixed isotropic and anisotropic thermal model 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 with anisotropic adps for all atoms except for water molecules above a certain adp cut off
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Displacement parameters | Biso mean: 11.2 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.119 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 27 / Occupancy sum hydrogen: 2215 / Occupancy sum non hydrogen: 2747 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→10 Å
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Refine LS restraints |
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