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- PDB-2wdr: E. coli succinate:quinone oxidoreductase (SQR) with pentachloroph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wdr | ||||||
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Title | E. coli succinate:quinone oxidoreductase (SQR) with pentachlorophenol bound | ||||||
![]() | (SUCCINATE DEHYDROGENASE ...) x 4 | ||||||
![]() | OXIDOREDUCTASE / SUCCINATE DEHYDROGENASE ACTIVITY / CELL INNER MEMBRANE / TRICARBOXYLIC ACID CYCLE / CELL MEMBRANE / METAL-BINDING / TRANSMEMBRANE / TRANSPORT / IRON-SULFUR / FLAVOPROTEIN / ELECTRON TRANSPORT / FAD / IRON / HEME | ||||||
Function / homology | ![]() : / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / oxidoreductase activity, acting on the CH-CH group of donors / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...: / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / oxidoreductase activity, acting on the CH-CH group of donors / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ruprecht, J. / Yankovskaya, V. / Maklashina, E. / Iwata, S. / Cecchini, G. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 596.3 KB | Display | ![]() |
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PDB format | ![]() | 496.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
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Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 105.7 KB | Display | |
Data in CIF | ![]() | 141.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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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.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() 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 8-129 MODELLED / Source: (gene. exp.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 24 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/TEO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PCI.gif)
![](data/chem/img/TEO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/PCI.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1M TRIS PH8.5, 0.1M LI2SO4, 0.1M NACL, 0.009% DDM, 12% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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→50.06 Å / Num. obs: 76421 / % possible obs: 99.3 % / Observed criterion σ(I): 6 / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 3.2→46.52 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.888 / SU B: 38.736 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.438 / 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: 47.98 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→46.52 Å
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Refine LS restraints |
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