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Yorodumi- PDB-6hli: wild-type NuoEF from Aquifex aeolicus - reduced form bound to NAD+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hli | ||||||
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Title | wild-type NuoEF from Aquifex aeolicus - reduced form bound to NAD+ | ||||||
Components | (NADH-quinone oxidoreductase subunit ...) x 2 | ||||||
Keywords | ELECTRON TRANSPORT / Complex I / NuoEF / electron transfer / Aquifex aeolicus | ||||||
Function / homology | Function and homology information Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus VF5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Gerhardt, S. / Friedrich, T. / Einsle, O. / Gnandt, E. / Schulte, M. / Fiegen, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I. Authors: Schulte, M. / Frick, K. / Gnandt, E. / Jurkovic, S. / Burschel, S. / Labatzke, R. / Aierstock, K. / Fiegen, D. / Wohlwend, D. / Gerhardt, S. / Einsle, O. / Friedrich, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hli.cif.gz | 479.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hli.ent.gz | 393 KB | Display | PDB format |
PDBx/mmJSON format | 6hli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/6hli ftp://data.pdbj.org/pub/pdb/validation_reports/hl/6hli | HTTPS FTP |
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-Related structure data
Related structure data | 6hl2C 6hl3C 6hl4C 6hlaC 6hljC 6hlmC 6q9cC 6q9gC 6q9jC 6q9kC 6r7pC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-NADH-quinone oxidoreductase subunit ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 18573.619 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoE, aq_574 / Production host: Escherichia coli (E. coli) / References: UniProt: O66842, NADH dehydrogenase (quinone) #2: Protein | Mass: 48523.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence contains C-terminal 6xHis Expressions-tag / Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli) / References: UniProt: O66841, NADH dehydrogenase (quinone) |
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-Non-polymers , 5 types, 256 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.61 Å3/Da / Density % sol: 52.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9 / Details: 0.1M Tris/HCl 0.1M Sodium citrate / PH range: 6.9 - 7.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 2016 / Details: VARIMAX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→116 Å / Num. obs: 57523 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 45.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.051 / Rsym value: 0.119 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8284 / CC1/2: 0.778 / Rpim(I) all: 0.351 / Rsym value: 0.757 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE Resolution: 2.38→60.3 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.343 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.345 / SU Rfree Blow DPI: 0.228 / SU Rfree Cruickshank DPI: 0.23
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Displacement parameters | Biso mean: 50.48 Å2
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Refinement step | Cycle: 1 / Resolution: 2.38→60.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.44 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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