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Yorodumi- PDB-6hla: wild-type NuoEF from Aquifex aeolicus - reduced form bound to NADH -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hla | ||||||
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Title | wild-type NuoEF from Aquifex aeolicus - reduced form bound to NADH | ||||||
Components | (NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 2 | ||||||
Keywords | ELECTRON TRANSPORT / Complex I / NuoEF / electron transfer / Aquifex aeolicus | ||||||
Function / homology | Function and homology information plasma membrane respiratory chain complex I / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6hla.cif.gz | 481.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hla.ent.gz | 406 KB | Display | PDB format |
PDBx/mmJSON format | 6hla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/6hla ftp://data.pdbj.org/pub/pdb/validation_reports/hl/6hla | HTTPS FTP |
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-Related structure data
Related structure data | 6hl2C 6hl3C 6hl4C 6hliC 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 (strain VF5) (bacteria) Strain: VF5 / 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 includes C-terminal 6xHis Expression-tag Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli) / References: UniProt: O66841, NADH dehydrogenase (quinone) |
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-Non-polymers , 7 types, 682 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: 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: 2.72 Å3/Da / Density % sol: 54.71 % |
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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: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 19, 2010 / Details: MIRRORS |
Radiation | Monochromator: DCCM crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→189.45 Å / Num. obs: 110071 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 21.09 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.143 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 4524 / Rsym value: 0.743 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INHOUSE Resolution: 1.9→99.2 Å / Cor.coef. Fo:Fc: 0.9301 / Cor.coef. Fo:Fc free: 0.9132 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.159 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.138
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Displacement parameters | Biso mean: 29.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→99.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 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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