+Open data
-Basic information
Entry | Database: PDB / ID: 1l0v | |||||||||
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Title | Quinol-Fumarate Reductase with Menaquinol Molecules | |||||||||
Components | (Fumarate reductase ...) x 4 | |||||||||
Keywords | OXIDOREDUCTASE / fumarate reductase / succinate dehydrogenase / complex II / quinol / membrane protein | |||||||||
Function / homology | Function and homology information plasma membrane fumarate reductase complex / succinate dehydrogenase activity / fermentation / anaerobic electron transport chain / fumarate metabolic process / : / succinate dehydrogenase / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...plasma membrane fumarate reductase complex / succinate dehydrogenase activity / fermentation / anaerobic electron transport chain / fumarate metabolic process / : / succinate dehydrogenase / 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 / MAD / Resolution: 3.3 Å | |||||||||
Authors | Iverson, T.M. / Luna-Chavez, C. / Croal, L.R. / Cecchini, G. / Rees, D.C. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystallographic studies of the Escherichia coli quinol-fumarate reductase with inhibitors bound to the quinol-binding site. Authors: Iverson, T.M. / Luna-Chavez, C. / Croal, L.R. / Cecchini, G. / Rees, D.C. #1: Journal: Science / Year: 1999 Title: Structure of the E. coli Fumarate Reductase Respiratory Complex Authors: Iverson, T.M. / Luna-Chavez, C. / Cecchini, G. / Rees, D.C. #2: Journal: Protein Expr.Purif. / Year: 2000 Title: Overexpression, Purification, and Crystallization of the Membrane-Bound Fumarate Reductase from Eschericia coli Authors: Luna-Chavez, C. / Iverson, T.M. / Rees, D.C. / Cecchini, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l0v.cif.gz | 399.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l0v.ent.gz | 321.1 KB | Display | PDB format |
PDBx/mmJSON format | 1l0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/1l0v ftp://data.pdbj.org/pub/pdb/validation_reports/l0/1l0v | HTTPS FTP |
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-Related structure data
Related structure data | 1kf6C 1kfyC 1fum C: citing same article (ref.) 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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3 |
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Unit cell |
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Details | heterotetramer: two complete heterotetramers are observed in each asymmetric unit |
-Components
-Fumarate reductase ... , 4 types, 8 molecules AMBNCODP
#1: Protein | Mass: 66057.555 Da / Num. of mol.: 2 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 #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 , 7 types, 18 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MQ7 / #11: Chemical | ChemComp-CE1 / |
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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: 3.79 Å3/Da / Density % sol: 67.53 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG 10000, MgAcetate, NaCitrate, DTT, EDTA, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.65 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 1998 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.65 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 49332 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 75 Å2 / Rsym value: 0.093 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 3.3→3.42 Å / Mean I/σ(I) obs: 6.5 / Rsym value: 0.277 / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 219456 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 90 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 6.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1FUM 1fum Resolution: 3.3→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.245 / Rfactor Rfree: 0.29 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.014 |