+Open data
-Basic information
Entry | Database: PDB / ID: 2b7s | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | R381K mutant of 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 / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity ...fumarate reductase (cytochrome) / fumarate reductase (quinol) / : / anaerobic electron transport chain / anaerobic respiration / steroid metabolic process / FMN binding / outer membrane-bounded periplasmic space / periplasmic space / oxidoreductase activity / electron transfer activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Shewanella frigidimarina (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2b7s.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2b7s.ent.gz | 110.8 KB | Display | PDB format |
PDBx/mmJSON format | 2b7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b7s_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2b7s_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 2b7s_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 2b7s_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b7s ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b7s | HTTPS FTP |
-Related structure data
Related structure data | 2b7rC 1qjdS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60599.227 Da / Num. of mol.: 1 / Mutation: R381K 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 |
---|
-Non-polymers , 5 types, 780 molecules
#2: Chemical | ChemComp-NA / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-FAD / | #5: Chemical | ChemComp-FUM / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.6 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. all: 35764 / Num. obs: 35478 / % possible obs: 99.2 % / Biso Wilson estimate: 15.504 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 4.7 / Num. unique all: 1765 / % possible all: 98.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QJD Resolution: 2.12→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.992 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15.472 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.122→2.177 Å / Total num. of bins used: 20
|