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Yorodumi- PDB-6rvh: NADH-dependent Coenzyme A Disulfide Reductase soaked with Menadione -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rvh | ||||||
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Title | NADH-dependent Coenzyme A Disulfide Reductase soaked with Menadione | ||||||
Components | NADH oxidase | ||||||
Keywords | OXIDOREDUCTASE / Coenzyme A Disulfide Reductase / NADH oxidation / flavoprotein / Menadione | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on NADH or NADPH / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Koepke, J. / Preu, J. | ||||||
Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2019 Title: Characterization and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus. Authors: Lencina, A.M. / Koepke, J. / Preu, J. / Muenke, C. / Gennis, R.B. / Michel, H. / Schurig-Briccio, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rvh.cif.gz | 361.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rvh.ent.gz | 293.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rvh_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6rvh_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6rvh_validation.xml.gz | 88.6 KB | Display | |
Data in CIF | 6rvh_validation.cif.gz | 111.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/6rvh ftp://data.pdbj.org/pub/pdb/validation_reports/rv/6rvh | HTTPS FTP |
-Related structure data
Related structure data | 6ruzC 6rvbC 3ntaS 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:
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-Components
#1: Protein | Mass: 47919.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT_C1484 / Production host: Escherichia coli (E. coli) References: UniProt: Q72HK3, Oxidoreductases; Acting on NADH or NADPH #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-VK3 / #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: 4.27 Å3/Da / Density % sol: 71.19 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES-Na, NaCl, FAD, dodecyl-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3→58.4 Å / Num. obs: 63717 / % possible obs: 95 % / Redundancy: 3.01 % / Rsym value: 0.294 / Net I/σ(I): 4.37 |
Reflection shell | Resolution: 3→3.1 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 6095 / Rsym value: 1.344 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nta Resolution: 3→58.346 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.45
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 26.688 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→58.346 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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