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Yorodumi- PDB-1nen: Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nen | ||||||
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Title | Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site | ||||||
Components | (Succinate dehydrogenase ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / membrane protein / respiratory complex / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / oxidoreductase activity, acting on the CH-CH group of donors / aerobic electron transport chain / anaerobic respiration ...plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / oxidoreductase activity, acting on the CH-CH group of donors / aerobic electron transport chain / anaerobic respiration / ubiquinone binding / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / aerobic respiration / tricarboxylic acid cycle / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Yankovskaya, V. / Horsefield, R. / Tornroth, S. / Luna-Chavez, C. / Miyoshi, H. / Leger, C. / Byrne, B. / Cecchini, G. / Iwata, S. | ||||||
Citation | Journal: Science / Year: 2003 Title: Architecture of succinate dehydrogenase and reactive oxygen species generation Authors: Yankovskaya, V. / Horsefield, R. / Tornroth, S. / Luna-Chavez, C. / Miyoshi, H. / Leger, C. / Byrne, B. / Cecchini, G. / Iwata, S. | ||||||
History |
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Remark 600 | HETEROGEN THE HET GROUP CDN WAS NAMED CARDIOLIPIN WHICH IS A GENERIC NAME FOR THIS TYPE OF LIPID. ...HETEROGEN THE HET GROUP CDN WAS NAMED CARDIOLIPIN WHICH IS A GENERIC NAME FOR THIS TYPE OF LIPID. THE 4 TAILS OF THE MOLECULE ARE DISORDERED IN THE STRUCTURE AND THEIR EXACT LENGTH CAN NOT ASCERTAINED MAKING IT DIFFICULT TO ASSIGN AN EXACT NAME. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nen.cif.gz | 227.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nen.ent.gz | 187.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1nen ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1nen | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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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) / Gene: SDHA OR B0723 OR Z0877 OR ECS0748 / Plasmid: pfas / Production host: Escherichia coli (E. coli) References: UniProt: P0AC41, succinate dehydrogenase, 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) / Gene: SDHB OR B0724 / Plasmid: pfas / Production host: Escherichia coli (E. coli) References: UniProt: P07014, succinate dehydrogenase, 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) / Gene: SDHC OR CYBA OR B0721 OR Z0875 OR ECS0746 / Plasmid: pfas / Production host: Escherichia coli (E. coli) / 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) / Gene: SDHD OR B0722 / Plasmid: pfas / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC44 |
-Non-polymers , 11 types, 151 molecules
#5: Chemical | ChemComp-OAA / | ||||||||||||||||||
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#6: Chemical | #7: Chemical | ChemComp-FAD / | #8: Chemical | ChemComp-FES / | #9: Chemical | ChemComp-SF4 / | #10: Chemical | ChemComp-F3S / | #11: Chemical | ChemComp-HEM / | #12: Chemical | ChemComp-DNT / | #13: Chemical | ChemComp-CDN / | #14: Chemical | ChemComp-EPH / | #15: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.86 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: Tris-HCl, CaCl2, PEG 400, BaCl2, ethylene glycol, DNP17, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. all: 43562 / Num. obs: 42735 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rsym value: 0.116 |
Reflection shell | Resolution: 2.9→2.96 Å / Rsym value: 0.428 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 119504 / Rmerge(I) obs: 0.116 |
Reflection shell | *PLUS % possible obs: 96.6 % / Rmerge(I) obs: 0.428 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→40 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 1 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 2.96 Å / Rfactor Rfree: 0.365 / Rfactor Rwork: 0.326 |