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Yorodumi- PDB-2bs4: GLU C180 -> ILE VARIANT QUINOL:FUMARATE REDUCTASE FROMWOLINELLA S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bs4 | ||||||
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Title | GLU C180 -> ILE VARIANT QUINOL:FUMARATE REDUCTASE FROMWOLINELLA SUCCINOGENES | ||||||
Components | (QUINOL-FUMARATE REDUCTASE ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / 2FE-2S / 3FE-4S / 4FE-4S / CITRIC ACID CYCLE / DIHAEM CYTOCHROME B / ELECTRON TRANSPORT / FAD / FLAVOPROTEIN / FUMARATE REDUCTASE / HEME / ION-SULPHUR PROTEIN / IRON / IRON-SULFUR / METAL-BINDING / RESPIRATORY CHAIN / SUCCINATE DEHYDROGENASE / TRANSMEMBRANE / TRICARBOXYLIC ACID CYCLE | ||||||
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: 2.76 Å | ||||||
Authors | Lancaster, C.R.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Experimental Support for the E-Pathway Hypothesis of Coupled Transmembrane Electron and Proton Transfer in Dihemic Quinol:Fumarate Reductase Authors: Lancaster, C.R.D. / Sauer, U.S. / Gross, R. / Haas, A.H. / Graf, J. / Schwalbe, H. / Maentele, W. / Simon, J. / Madej, G. #1: Journal: FEBS Lett. / Year: 2003 Title: Wolinella Succinogenes Quinol:Fumarate Reductase and its Comparison to E. Coli Succinate:Quinone Reductase Authors: Lancaster, C.R.D. #2: Journal: Biochim.Biophys.Acta / Year: 2002 Title: Wolinella Succinogenes Quinol:Fumarate Reductase -2.2 Angstrom Resolution Crystal Structure and the E-Pathway Hypothesis of Coupled Transmembrane Proton and Electron Transfer Authors: Lancaster, C.R.D. #3: 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. #4: 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. #5: 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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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bs4.cif.gz | 485.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bs4.ent.gz | 387.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/2bs4 ftp://data.pdbj.org/pub/pdb/validation_reports/bs/2bs4 | HTTPS FTP |
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-Related structure data
Related structure data | 2bs3C 2bs2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-QUINOL-FUMARATE REDUCTASE ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 72825.055 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: FAD COVALENTLY BOUND TO HIS A43 BY AN 8-ALPHA-(N-EPSILON-HISTIDYL) BOND Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17412, succinate dehydrogenase #2: Protein | Mass: 27197.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17596, succinate dehydrogenase #3: Protein | Mass: 29743.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) WOLINELLA SUCCINOGENES (bacteria) / References: UniProt: P17413, succinate dehydrogenase |
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-Sugars , 1 types, 2 molecules
#11: Sugar |
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-Non-polymers , 9 types, 490 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-HEM / #8: Chemical | #9: Chemical | #10: Chemical | #12: Chemical | #13: Water | ChemComp-HOH / | |
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-Details
Compound details | FUNCTION: ESSENTIAL FOR FUMARATE RESPIRATIOSequence details | E180I VARIANT FOR CHAINS C AND F. | |
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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: 3.4 Å3/Da / Density % sol: 62.4 % |
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Crystal grow | pH: 6 / Details: pH 6.00 |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 26, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→29.71 Å / Num. obs: 79393 / % possible obs: 87.3 % / Observed criterion σ(I): -1 / Redundancy: 2.2 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.76→2.83 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.2 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BS2 Resolution: 2.76→29.65 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2091334.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: THIS ENTRY CONTAINS ATOMS WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN REFINED.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.5046 Å2 / ksol: 0.289152 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.76→29.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.93 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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