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- PDB-2ws3: Crystal structure of the E. coli succinate:quinone oxidoreductase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ws3 | ||||||
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Title | Crystal structure of the E. coli succinate:quinone oxidoreductase (SQR) SdhD Tyr83Phe mutant | ||||||
![]() | (SUCCINATE DEHYDROGENASE ...) x 4 | ||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSPORT | ||||||
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: Succinate Dehydrogenase Activity 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 | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 108.6 KB | Display | |
Data in CIF | ![]() | 145.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wdqS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
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.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 26800.912 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 12858.438 Da / Num. of mol.: 3 / Mutation: YES 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/NA.gif)
![](data/chem/img/TEO.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/CBE.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TEO.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/F3S.gif)
![](data/chem/img/CBE.gif)
![](data/chem/img/HEM.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN D, TYR 83 TO PHE ENGINEERED RESIDUE IN CHAIN H, TYR 83 TO PHE ...ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.67 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.03 Å / Num. obs: 71105 / % possible obs: 99.8 % / Observed criterion σ(I): 6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WDQ Resolution: 3.2→49.03 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.885 / SU B: 52.792 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→49.03 Å
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Refine LS restraints |
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