+Open data
-Basic information
Entry | Database: PDB / ID: 2b76 | ||||||
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Title | E. coli Quinol fumarate reductase FrdA E49Q mutation | ||||||
Components | (Fumarate reductase ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / fumarate reductase / succinate dehydrogenase / electron transfer / respiration / krebs cycle / membrane protein | ||||||
Function / homology | Function and homology information plasma membrane fumarate reductase complex / fumarate reductase (quinol) / succinate dehydrogenase activity / fermentation / : / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration ...plasma membrane fumarate reductase complex / fumarate reductase (quinol) / succinate dehydrogenase activity / fermentation / : / fumarate metabolic process / succinate dehydrogenase / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / bacterial-type flagellum assembly / tricarboxylic acid cycle / FAD binding / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA damage response / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Maklashina, E. / Iverson, T.M. / Sher, Y. / Kotlyar, V. / Mirza, O. / Andrell, J. / Hudson, J.M. / Armstrong, F.A. / Cecchini, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Fumarate Reductase and Succinate Oxidase Activity of Escherichia coli Complex II Homologs Are Perturbed Differently by Mutation of the Flavin Binding Domain Authors: Maklashina, E. / Iverson, T.M. / Sher, Y. / Kotlyar, V. / Andrell, J. / Mirza, O. / Hudson, J.M. / Armstrong, F.A. / Rothery, R.A. / Weiner, J.H. / Cecchini, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b76.cif.gz | 432.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b76.ent.gz | 342 KB | Display | PDB format |
PDBx/mmJSON format | 2b76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b76 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b76 | HTTPS FTP |
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-Related structure data
Related structure data | 1kf6S 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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2 |
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Unit cell |
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Details | The biological unit is a single heterotetramer. There are two heterotetramers in each asymmetric unit |
-Components
-Fumarate reductase ... , 4 types, 8 molecules AMBNCODP
#1: Protein | Mass: 66056.570 Da / Num. of mol.: 2 / Mutation: E49Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FrdA / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: GenBank: P00363, UniProt: P00363*PLUS #2: Protein | Mass: 27021.885 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: frdB / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 References: UniProt: P00364, UniProt: P0AC47*PLUS, succinate dehydrogenase #3: Protein | Mass: 14898.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: frdC / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q0 #4: Protein | Mass: 13118.870 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: frdD / Plasmid: PH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P0A8Q3 |
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-Non-polymers , 6 types, 12 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Mg Acetate, PEG 5000 MME, Na Citrate, EDTA, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 47106 / % possible obs: 88.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.098 |
Reflection shell | Resolution: 3.3→3.35 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.1 / % possible all: 73.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1KF6 Resolution: 3.3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 10 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.505 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Xplor file |
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