+Open data
-Basic information
Entry | Database: PDB / ID: 1e7p | |||||||||
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Title | QUINOL:FUMARATE REDUCTASE FROM WOLINELLA SUCCINOGENES | |||||||||
Components | (Fumarate reductase ...) x 3 | |||||||||
Keywords | OXIDOREDUCTASE / SUCCINATE DEHYDROGENASE / RESPIRATORY CHAIN / CITRIC ACID CYCLE / FLAVOPROTEIN / IRON- SULPHUR PROTEIN IRON- SULPHUR PROTEIN / DIHAEM CYTOCHROME B | |||||||||
Function / homology | Function and homology information : / succinate dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding ...: / succinate dehydrogenase / oxidoreductase activity, acting on the CH-CH group of donors / 3 iron, 4 sulfur cluster binding / electron transport chain / respirasome / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Wolinella succinogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||
Authors | Lancaster, C.R.D. / Kroeger, A. | |||||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: A Third Crystal Form of Wolinella Succinogenes Quinol:Fumarate Reductase Reveals Domain Closure at the Site of Fumarate Reduction Authors: Lancaster, C.R.D. / Gross, R. / Simon, J. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Essential Role of Glu-C66 for Menaquinol Oxidation Indicates Transmembrane Electrochemical Potential Generation by Wolinella Succinogenes Fumarate Reductase Authors: Lancaster, C.R.D. / Gross, R. / Haas, A. / Ritter, M. / Maentele, W. / Simon, J. / Kroeger, A. #2: Journal: Nature / Year: 1999 Title: Structure of Fumarate Reductase from Wolinella Succinogenes at 2.2 Angstroms Resolution Authors: Lancaster, C.R.D. / Kroeger, A. / Auer, M. / Michel, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e7p.cif.gz | 925.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e7p.ent.gz | 746.6 KB | Display | PDB format |
PDBx/mmJSON format | 1e7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/1e7p ftp://data.pdbj.org/pub/pdb/validation_reports/e7/1e7p | HTTPS FTP |
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-Related structure data
Related structure data | 1qla 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Fumarate reductase ... , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 72825.055 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 8-ALPHA-[-N-EPSILON-HISTIDYL] COVALENT BOND BETWEEN FLAVIN ADENINE DINUCLEOTIDE (FAD) AND HIS 43 Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: frdA, WS0831 / Production host: Wolinella succinogenes (bacteria) / References: UniProt: P17412, fumarate reductase (quinol) #2: Protein | Mass: 27197.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: frdB, WS0830 / Production host: Wolinella succinogenes (bacteria) / References: UniProt: P17596, succinate dehydrogenase #3: Protein | Mass: 29758.070 Da / Num. of mol.: 4 / Mutation: E66Q Source method: isolated from a genetically manipulated source Details: HAEM AXIAL LIGANDS - HIS 44, HIS 93, HIS 143 HIS 182 Source: (gene. exp.) Wolinella succinogenes (bacteria) Strain: ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W Gene: frdC, WS0832 / Variant: FRDC-E66Q / Production host: Wolinella succinogenes (bacteria) / References: UniProt: P17413 |
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-Sugars , 1 types, 4 molecules
#11: Sugar | ChemComp-LMT / |
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-Non-polymers , 7 types, 32 molecules
#4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-MLA / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-FES / #8: Chemical | ChemComp-F3S / #9: Chemical | ChemComp-SF4 / #10: Chemical | ChemComp-HEM / |
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-Details
Compound details | CHAINS: C, F, I, L CONTAIN ENGINEERED |
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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: 3.46 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.4 / Method: vapor diffusionDetails: used microseeding, Lancaster, C.R.D., (1999) Nature, 402, 377. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 275 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.958 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 9, 2000 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.958 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 102882 / % possible obs: 80.8 % / Observed criterion σ(I): -1 / Redundancy: 2.7 % / Biso Wilson estimate: 65.4 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.1→3.29 Å / Redundancy: 1.97 % / Mean I/σ(I) obs: 2 / Rsym value: 0.26 / % possible all: 61.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QLA 1qla Resolution: 3.1→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: N(OBS)/N(PAR) = 1.57
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Solvent computation | Bsol: 48.4 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.477 |