+Open data
-Basic information
Entry | Database: PDB / ID: 2b7r | |||||||||
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Title | Structure of E378D mutant flavocytochrome c3 | |||||||||
Components | Fumarate reductase flavoprotein subunit | |||||||||
Keywords | OXIDOREDUCTASE / flavocytochrome c3 / fumarate reductase / proton delivery | |||||||||
Function / homology | Function and homology information fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space ...fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / succinate dehydrogenase (quinone) activity / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Shewanella frigidimarina (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Pankhurst, K.L. / Mowat, C.G. / Rothery, E.L. / Miles, C.S. / Walkinshaw, M.D. / Reid, G.A. / Chapman, S.K. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: A Proton Delivery Pathway in the Soluble Fumarate Reductase from Shewanella frigidimarina. Authors: Pankhurst, K.L. / Mowat, C.G. / Rothery, E.L. / Hudson, J.M. / Jones, A.K. / Miles, C.S. / Walkinshaw, M.D. / Armstrong, F.A. / Reid, G.A. / Chapman, S.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b7r.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b7r.ent.gz | 116.3 KB | Display | PDB format |
PDBx/mmJSON format | 2b7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b7r_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 2b7r_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 2b7r_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 2b7r_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b7r ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b7r | HTTPS FTP |
-Related structure data
Related structure data | 2b7sC 1qjdS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60613.219 Da / Num. of mol.: 1 / Mutation: E378D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Gene: FCC / Plasmid: pMMB503EH / Production host: Shewanella frigidimarina (bacteria) / Strain (production host): EG301 References: UniProt: Q02469, UniProt: P0C278*PLUS, succinate dehydrogenase |
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-Non-polymers , 5 types, 1091 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-FUM / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M TrisHCl, 80mM NaCl, 10mM Na fumarate, 15% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 73408 / Num. obs: 72178 / % possible obs: 98.4 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 6.9 / Num. unique all: 6862 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QJD Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.466 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.322 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.698→1.742 Å / Total num. of bins used: 20
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