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Yorodumi- PDB-2wdv: E. coli succinate:quinone oxidoreductase (SQR) with an empty quin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wdv | ||||||
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Title | E. coli succinate:quinone oxidoreductase (SQR) with an empty quinone- binding pocket | ||||||
Components | (SUCCINATE DEHYDROGENASE ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / SUCCINATE DEHYDROGENASE ACTIVITY / CELL INNER MEMBRANE / TRICARBOXYLIC ACID CYCLE / METAL-BINDING / TRANSMEMBRANE / FLAVOPROTEIN / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / aerobic electron transport chain / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / aerobic electron transport chain / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / ubiquinone 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 / OTHER / Resolution: 3.2 Å | ||||||
Authors | Ruprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure of Escherichia Coli Succinate:Quinone Oxidoreductase with an Occupied and Empty Quinone- Binding Site. Authors: Ruprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wdv.cif.gz | 594.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wdv.ent.gz | 494.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wdv ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wdv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-SUCCINATE DEHYDROGENASE ... , 4 types, 12 molecules AEIBFJCGKDHL
#1: Protein | Mass: 64502.766 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: FAD ATOM C8M IS COVALENTLY LINKED TO NE2 OF SDHA HIS45 Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35 References: UniProt: P0AC41, succinate dehydrogenase, succinate dehydrogenase #2: Protein | Mass: 26800.912 Da / Num. of mol.: 3 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, succinate dehydrogenase #3: Protein | Mass: 14313.100 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: RESIDUES 8-128 MODELLED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35 / References: UniProt: P69054, succinate dehydrogenase #4: Protein | Mass: 12874.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: RESIDUES 11-115 MODELLED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PFAS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DW35 / References: UniProt: P0AC44, succinate dehydrogenase |
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-Non-polymers , 7 types, 21 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | |
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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: 3.16 Å3/Da / Density % sol: 61.1 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 0.1M TRIS PH 8.5, 0.1M MGSO4, 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→52.85 Å / Num. obs: 76081 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 3.2→51.85 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.884 / SU B: 40.751 / SU ML: 0.334 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY FOR THE N-TERMINUS OF SDH C (RESIDUES 1-7 OF CHAINS C, G, K) AND THE N-TERMINUS OF SDHD (RESIDUES 1-10 OF CHAINS D, H AND L) WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DENSITY FOR THE N-TERMINUS OF SDH C (RESIDUES 1-7 OF CHAINS C, G, K) AND THE N-TERMINUS OF SDHD (RESIDUES 1-10 OF CHAINS D, H AND L) WAS WEAK AND THESE REGIONS ARE NOT INCLUDED IN THE MODEL. THE SIDE CHAIN OF SDHD TRP113 IS TRUNCATED AT THE CBETA ATOM SINCE DENSITY FOR THE SIDE CHAIN WAS POOR.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.96 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→51.85 Å
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Refine LS restraints |
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