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Yorodumi- PDB-3fwh: Structure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fwh | ||||||
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Title | Structure of haloalkane dehalogenase mutant Dha15 (I135F/C176Y) from Rhodococcus rhodochrous | ||||||
Components | Haloalkane dehalogenase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase core / helical cap domain / catalytic triad (Asp106 / His272 / Glu130) / mutant / I135F / C176Y / 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: 1.22 Å | ||||||
Authors | Gavira, J.A. / Stsiapanava, A. / Kuty, M. / Dohnalek, J. / Lapkouski, M. / 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 | 3fwh.cif.gz | 161.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fwh.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fwh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/3fwh ftp://data.pdbj.org/pub/pdb/validation_reports/fw/3fwh | HTTPS FTP |
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-Related structure data
Related structure data | 3fbwC 3g9xC 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: 34204.914 Da / Num. of mol.: 1 / Mutation: I135F, C176Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: NCIMB 13064 / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A3G3, haloalkane dehalogenase | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | #4: Chemical | ChemComp-IPA / | #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: 2.05 Å3/Da / Density % sol: 40.05 % |
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Crystal grow | Temperature: 277 K / pH: 7.5 Details: 25 % PEG 4 000, 8 % iso-propanol and 100 mM Na-Acetate, pH 7.5, 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: 1.15 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: MIRROR: ELLIPTICALLY BENT 12 QUARTZ SEGMENTS |
Radiation | Monochromator: MONOCHROMATOR: GE(111) TRIANGULAR BENT COMPRESSING 7 FANKUCHEN CUT Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 77114 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 6.8 / % possible all: 45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BN6 Resolution: 1.22→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.769 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 8.817 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.25 Å / Total num. of bins used: 20
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