+Open data
-Basic information
Entry | Database: PDB / ID: 3cir | ||||||
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Title | E. coli Quinol fumarate reductase FrdA T234A mutation | ||||||
Components | (Fumarate reductase ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / electron transport / Tricarboxylic acid cycle | ||||||
Function / homology | Function and homology information : / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / anaerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...: / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / anaerobic electron transport chain / 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: 3.65 Å | ||||||
Authors | Tomasiak, T.M. / Maklashina, E. / Cecchini, G. / Iverson, T.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: A threonine on the active site loop controls transition state formation in Escherichia coli respiratory complex II. Authors: Tomasiak, T.M. / Maklashina, E. / Cecchini, G. / Iverson, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cir.cif.gz | 390.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cir.ent.gz | 313.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cir_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3cir_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3cir_validation.xml.gz | 88.7 KB | Display | |
Data in CIF | 3cir_validation.cif.gz | 117.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3cir ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cir | HTTPS FTP |
-Related structure data
Related structure data | 2b76S 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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-Components
-Fumarate reductase ... , 4 types, 8 molecules AMBNCODP
#1: Protein | Mass: 66027.523 Da / Num. of mol.: 2 / Mutation: T234A 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: UniProt: P00363, succinate dehydrogenase #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: P0AC47, 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, succinate dehydrogenase #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, succinate dehydrogenase |
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-Non-polymers , 4 types, 8 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: 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: 3.6 Å3/Da / Density % sol: 65.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 10% PEG 5000 MME, 0.250M magnesium acetate, 100mM citric acid, 0.001M EDTA, 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: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→266 Å / Num. all: 40327 / Num. obs: 32532 / % possible obs: 80.7 % / Observed criterion σ(F): -3 / Rsym value: 0.39 |
Reflection shell | Resolution: 3.65→3.71 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.391 / % possible all: 55.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B76 Resolution: 3.65→266 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.65→266 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.65→3.76 Å
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