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Yorodumi- PDB-9fe8: Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fe8 | ||||||
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Title | Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus | ||||||
Components | (NADH-quinone oxidoreductase subunit ...) x 2 | ||||||
Keywords | ELECTRON TRANSPORT / Complex I / respiratory chain / NADH-ubiquinone oxidoreductase / bioenergetics | ||||||
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 VF5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Wohlwend, D. / Friedrich, T. / Goeppert-Asadollahpour, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2024 Title: Structural robustness of the NADH binding site in NADH:ubiquinone oxidoreductase (complex I). Authors: Goppert-Asadollahpour, S. / Wohlwend, D. / Friedrich, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fe8.cif.gz | 626.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fe8.ent.gz | 395.1 KB | Display | PDB format |
PDBx/mmJSON format | 9fe8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fe8_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 9fe8_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 9fe8_validation.xml.gz | 46.1 KB | Display | |
Data in CIF | 9fe8_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/9fe8 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/9fe8 | HTTPS FTP |
-Related structure data
Related structure data | 9fdjC 9fdkC 9fdvC 9fe0C 9fe5C 9fe7C 9feaC 9fifC 9fihC 9fiiC 9fijC 9filC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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 / Plasmid: pET-28b(+)::nuoEFhis_P228R / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: O66842, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions #2: Protein | Mass: 48583.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The C-terminal sequence AGHHHHHH is an artificial affinity tag used for affinity purification of the NuoEF complex Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Gene: nuoF, aq_573 / Plasmid: pET-28b(+)::nuoEFhis_P228R / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) References: UniProt: O66841, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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-Non-polymers , 8 types, 502 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NA / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-MPO / | #10: 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: 2.6 Å3/Da / Density % sol: 52.62 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 100 mM BisTris pH 6.3, 1.65 M ammonium sulfate, 150 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→49.638 Å / Num. obs: 59973 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.996 / Rpim(I) all: 0.068 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.34→2.4 Å / Num. unique obs: 4575 / CC1/2: 0.761 / Rpim(I) all: 0.508 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→49.638 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 14.879 / SU ML: 0.174 / Cross valid method: FREE R-VALUE / ESU R: 0.331 / ESU R Free: 0.205 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.243 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→49.638 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / 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 | Selection: ALL |