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Yorodumi- PDB-3g9x: Structure of haloalkane dehalogenase DhaA14 mutant I135F from Rho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g9x | ||||||
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Title | Structure of haloalkane dehalogenase DhaA14 mutant I135F from Rhodococcus rhodochrous | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / helical cap domain / catalytic triad (Asp106 / His272 / Glu130) / mutant / I135F / haloalkanes / Detoxification | ||||||
Function / homology | Function and homology information haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Gavira, J.A. / Stsiapanava, A. / Kuty, M. / Lapkouski, M. / Dohnalek, J. / Kuta Smatanova, I. | ||||||
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. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Crystals of dhaa mutants from rhodococcus rhodochrous ncimb 13064 diffracted to ultrahigh resolution: crystallization and preliminary diffraction analysis Authors: Stsiapanava, A. / Koudelakova, T. / Lapkouski, M. / Pavlova, M. / Damborsky, J. / Kuta Smatanova, I. #2: Journal: To be Published Title: Pathways and Mechanisms for Product Release in Engineered Haloalkane Dehalogenase DhaA Explored using Classical and Random Acceleration Molecular Dynamics Simulations Authors: Klvana, M. / Pavlova, M. / Koudelakova, T. / Chaloupkova, R. / Dvorak, P. / Stsiapanava, A. / Kuty, M. / Kuta Smatanova, I. / Dohnalek, J. / Kulhanek, P. / Wade, R.C. / Damborsky, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g9x.cif.gz | 149.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g9x.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g9x_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 3g9x_full_validation.pdf.gz | 449.7 KB | Display | |
Data in XML | 3g9x_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3g9x_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g9x ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g9x | HTTPS FTP |
-Related structure data
Related structure data | 3fbwC 3fwhC 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: 34144.883 Da / Num. of mol.: 1 / Mutation: I135F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: NCIMB 13064 / Gene: dhaA / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G3, haloalkane dehalogenase |
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#2: Chemical | ChemComp-IPA / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-CL / |
#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: 2.14 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 277 K / pH: 9 Details: [protein]=7-10 mg/ml in 50mM Tris-HCl buffer pH 7.5; [Precipitant]=25% PEG 4000, 8% 2-propanol in 100mM sodium acetate., 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: X11 / Wavelength: 0.8158 |
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: 0.95→30 Å / Num. obs: 163495 / % possible obs: 94.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 0.95→0.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.418 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BN6 Resolution: 0.95→10 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.984 / Num. parameters: 25397 / Num. restraintsaints: 32628 / SU B: 0.408 / SU ML: 0.011 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: ENGH AND HUBER Details: REFINEMENT IN SHELXL97 WITH ANISOTROPIC ADPS FOR ALL PROTEIN ATOMS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.763 Å2
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Refine analyze | Num. disordered residues: 64 / Occupancy sum hydrogen: 2132.7 / Occupancy sum non hydrogen: 2881.55 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.95→0.975 Å / Total num. of bins used: 20
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