+Open data
-Basic information
Entry | Database: PDB / ID: 6saq | ||||||||||||
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Title | wild-type NuoEF from Aquifex aeolicus bound to NADH-OH | ||||||||||||
Components | (NADH-quinone oxidoreductase subunit ...) x 2 | ||||||||||||
Keywords | ELECTRON TRANSPORT / NADH:ubiquinone Oxidoreductase / Complex I | ||||||||||||
Function / homology | Function and homology information Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / respiratory chain complex I / quinone binding / NADH dehydrogenase (ubiquinone) activity / 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: 2.02 Å | ||||||||||||
Authors | Gerhardt, S. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Structural Basis for Inhibition of ROS-Producing Respiratory Complex I by NADH-OH. Authors: Friedrich, T. / Vranas, M. / Wohlwend, D. / Qiu, D. / Gerhardt, S. / Trncik, C. / Pervaiz, M. / Ritter, K. / Steimle, S. / Randazzo, A. / Einsle, O. / Gunther, S. / Jessen, H.J. / Kotlyar, A. #1: 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 | 6saq.cif.gz | 484.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6saq.ent.gz | 395.5 KB | Display | PDB format |
PDBx/mmJSON format | 6saq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6saq_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6saq_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6saq_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 6saq_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/6saq ftp://data.pdbj.org/pub/pdb/validation_reports/sa/6saq | HTTPS FTP |
-Related structure data
Related structure data | 6hlmS S: Starting model for refinement |
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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 Details: contains Iron-sulphur cluster FES Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: nuoE, aq_574 / Production host: Escherichia coli (E. coli) References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions #2: Protein | Mass: 48523.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: contains FMN, Iron-Sulfur cluster and C-terminal Histag Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: nuoF, aq_573 / Production host: Escherichia coli (E. coli) References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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-Non-polymers , 6 types, 620 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 52.92 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 8000, Ethylen glycol, 0.1M MES-imidazole |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→116.9 Å / Num. obs: 92408 / % possible obs: 99.9 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.05 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.02→2.13 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 13438 / CC1/2: 0.741 / Rpim(I) all: 0.352 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HLM Resolution: 2.02→29.22 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.12
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Displacement parameters | Biso mean: 37.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→29.22 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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