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Yorodumi- PDB-5ogt: Thermus scotoductus SA-01 Ene-reductase triple mutant TsER_C25D_I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogt | ||||||
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Title | Thermus scotoductus SA-01 Ene-reductase triple mutant TsER_C25D_I67T_A102H | ||||||
Components | Chromate reductase | ||||||
Keywords | OXIDOREDUCTASE / Ene-reductase Old yellow enzyme C25D_I67T_A102H | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus scotoductus SA-01 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Opperman, D.J. / Hoebenreich, S. / Nett, N. | ||||||
Citation | Journal: To Be Published Title: Thermus scotoductus SA-01 Ene-reductase triple mutant TsER_C25D_I67T_A102H Authors: Opperman, D.J. / Hoebenreich, S. / Nett, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ogt.cif.gz | 282.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogt.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ogt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogt ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogt | HTTPS FTP |
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-Related structure data
Related structure data | 5nuxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38092.832 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus scotoductus SA-01 (bacteria) / Gene: chrR / Plasmid: pET22-b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: B0JDW3, UniProt: E8PRF1*PLUS #2: Chemical | ChemComp-FMN / #3: 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: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20,000 |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→69.65 Å / Num. obs: 85031 / % possible obs: 99.5 % / Redundancy: 2.9 % / CC1/2: 0.92 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.127 / Rrim(I) all: 0.225 / Net I/σ(I): 4.3 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NUX Resolution: 2.3→69.65 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.594 / SU ML: 0.182 / SU R Cruickshank DPI: 0.2721 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.215 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 66.36 Å2 / Biso mean: 22.044 Å2 / Biso min: 5.62 Å2
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Refinement step | Cycle: final / Resolution: 2.3→69.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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