+Open data
-Basic information
Entry | Database: PDB / ID: 5od3 | ||||||
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Title | Crystal structure of R. ruber ADH-A, mutant Y54G, L119Y | ||||||
Components | Alcohol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / alcohol dehydrogenase mutant variant / NADH-dependent / Zn2+-dependent / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodococcus sp. M8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Dobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M. | ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases Authors: Maurer, D. / Enugala, T.R. / Hamnevik, E. / Bauer, P. / Luking, M. / Petrovic, D. / Hillier, H. / Kamerlin, S.C.L. / Dobritzsch, D. / Widersten, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5od3.cif.gz | 285.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5od3.ent.gz | 231.5 KB | Display | PDB format |
PDBx/mmJSON format | 5od3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/5od3 ftp://data.pdbj.org/pub/pdb/validation_reports/od/5od3 | HTTPS FTP |
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-Related structure data
Related structure data | 6fg0C 3jv7S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 36043.914 Da / Num. of mol.: 4 / Mutation: Y54G, L119Y Source method: isolated from a genetically manipulated source Details: C-terminal His-tag / Source: (gene. exp.) Rhodococcus sp. M8 (bacteria) / Gene: BKE56_025765 / Plasmid: pGT7ADHA-5H / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A1Q8I6M1 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 18% (w/v) PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 10 mM MgCl2, 7.5 mM 4'-Bromo-trifluoroacetophenone, 8 mg/ml ADH-A |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→29.56 Å / Num. obs: 127660 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.072 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5876 / CC1/2: 0.524 / Rpim(I) all: 0.509 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3jv7 Resolution: 1.83→29.56 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.064 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.112 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.541 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→29.56 Å
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Refine LS restraints |
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