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Yorodumi- PDB-4r81: NAD(P)H:quinone oxidoreductase from Methanothermobacter marburgensis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r81 | ||||||
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Title | NAD(P)H:quinone oxidoreductase from Methanothermobacter marburgensis | ||||||
Components | NADH dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / flavodoxin-like/fold / FMN / NAD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Methanothermobacter marburgensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ullmann, E. / Tan, T.C. / Herwig, C. / Divne, C. / Spadiut, O. | ||||||
Citation | Journal: Biosci.Rep. / Year: 2014 Title: A novel cytosolic NADH:quinone oxidoreductase from Methanothermobacter marburgensis. Authors: Ullmann, E. / Tan, T.C. / Gundinger, T. / Herwig, C. / Divne, C. / Spadiut, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r81.cif.gz | 336.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r81.ent.gz | 275.3 KB | Display | PDB format |
PDBx/mmJSON format | 4r81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/4r81 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r81 | HTTPS FTP |
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-Related structure data
Related structure data | 3lcmS 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: 23571.502 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter marburgensis (archaea) Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / Gene: MTBMA_c07320 / Plasmid: pET21d+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9PVS9 #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: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M NaCl, 0.1 M Bis-Tris, 25% PEG3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2014 / Details: mirrors |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.34 Å / Num. all: 120455 / Num. obs: 120455 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.5→1.6 Å / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LCM Resolution: 1.5→45.967 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 22.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.967 Å
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Refine LS restraints |
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LS refinement shell |
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