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Yorodumi- PDB-2acz: Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2acz | ||||||
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Title | Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site | ||||||
Components | (Succinate dehydrogenase ...) x 4 | ||||||
Keywords | Oxidoreductase/Electron transport / MEMBRANE PROTEIN / Aerobic reparatory Complex II / SQR / succinate:ubiquinone oxidoreductase / AA5 / AT5 / Atpenin A5 / SDH / succinate dehydrogenase / Oxidoreductase-Electron transport COMPLEX | ||||||
Function / homology | Function and homology information : / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...: / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / respiratory electron transport chain / electron transport chain / aerobic respiration / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 Å | ||||||
Authors | Horsefield, R. / Yankovskaya, V. / Sexton, G. / Whittingham, W. / Shiomi, K. / Omura, S. / Byrne, B. / Cecchini, G. / Iwata, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction. Authors: Horsefield, R. / Yankovskaya, V. / Sexton, G. / Whittingham, W. / Shiomi, K. / Omura, S. / Byrne, B. / Cecchini, G. / Iwata, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2acz.cif.gz | 231.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2acz.ent.gz | 179.8 KB | Display | PDB format |
PDBx/mmJSON format | 2acz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2acz_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2acz_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2acz_validation.xml.gz | 49.2 KB | Display | |
Data in CIF | 2acz_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/2acz ftp://data.pdbj.org/pub/pdb/validation_reports/ac/2acz | HTTPS FTP |
-Related structure data
Related structure data | 1nekS 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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Unit cell |
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-Components
-Succinate dehydrogenase ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 64502.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 References: UniProt: P10444, UniProt: P0AC41*PLUS, succinate dehydrogenase |
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#2: Protein | Mass: 26800.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P07014, succinate dehydrogenase |
#3: Protein | Mass: 14313.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P69054 |
#4: Protein | Mass: 12874.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P10445, UniProt: P0AC44*PLUS |
-Non-polymers , 8 types, 8 molecules
#5: Chemical | ChemComp-OAA / |
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#6: Chemical | ChemComp-FAD / |
#7: Chemical | ChemComp-FES / |
#8: Chemical | ChemComp-SF4 / |
#9: Chemical | ChemComp-F3S / |
#10: Chemical | ChemComp-HEB / |
#11: Chemical | ChemComp-AT5 / |
#12: Chemical | ChemComp-CDN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 68.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: Tris-HCl, cacium chloride, Peg 400, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. all: 34954 / Num. obs: 34114 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.36 % / Rsym value: 0.078 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 3.1→3.16 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.337 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1NEK Resolution: 3.1→40 Å / Cross valid method: THROUGHOUT / σ(F): -2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 73.7 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.16 Å / Rfactor Rfree: 0.429 / Rfactor Rwork: 0.376 |