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Yorodumi- PDB-5o9d: Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o9d | ||||||
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Title | Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43H, H39Y | ||||||
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: 1.79 Å | ||||||
Authors | Dobritzsch, D. / Maurer, D. / Hamnevik, E. / Enugala, T.R. / Widersten, M. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: FEBS J. / Year: 2017 Title: Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer. Authors: Hamnevik, E. / Enugala, T.R. / Maurer, D. / Ntuku, S. / Oliveira, A. / 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 | 5o9d.cif.gz | 525.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o9d.ent.gz | 434.2 KB | Display | PDB format |
PDBx/mmJSON format | 5o9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o9d_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5o9d_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5o9d_validation.xml.gz | 61.5 KB | Display | |
Data in CIF | 5o9d_validation.cif.gz | 91.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9d ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9d | HTTPS FTP |
-Related structure data
Related structure data | 5o8hC 5o8qC 5o9fC 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: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 35968.887 Da / Num. of mol.: 4 / Mutation: Y294F, W295A, Y54F, F43H, H39Y Source method: isolated from a genetically manipulated source Details: C-terminal His-tag, 5 mutations as compared to wildtype ADH-A sequence Source: (gene. exp.) Rhodococcus sp. M8 (bacteria) / Gene: BKE56_025765 / Plasmid: pGT7ADHA-5H / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A1Q8I6M1 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-9ON / ( #5: 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: 2.36 Å3/Da / Density % sol: 47.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 17% PAA5100, 0.1 M Tris pH 8, 4 mM NAD+, 10 mM MgCl2, 7.5 mg/ml ADH-A |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→28.31 Å / Num. obs: 137475 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.072 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.79→1.82 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6245 / CC1/2: 0.573 / Rpim(I) all: 0.441 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3jv7 Resolution: 1.79→28.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.688 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.103 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.03 Å2
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Refinement step | Cycle: 1 / Resolution: 1.79→28.3 Å
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Refine LS restraints |
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