+Open data
-Basic information
Entry | Database: PDB / ID: 2nvf | ||||||
---|---|---|---|---|---|---|---|
Title | Soluble domain of Rieske Iron-Sulfur protein. | ||||||
Components | Ubiquinol-cytochrome c reductase iron-sulfur subunit | ||||||
Keywords | OXIDOREDUCTASE / Rieske [2Fe-2S] protein | ||||||
Function / homology | Function and homology information quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / 2 iron, 2 sulfur cluster binding / intracellular membrane-bounded organelle / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodobacter sphaeroides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kolling, D. / Brunzelle, J. / Lhee, S. / Crofts, A.R. / Nair, S.K. | ||||||
Citation | Journal: Structure / Year: 2007 Title: Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters. Authors: Kolling, D.J. / Brunzelle, J.S. / Lhee, S. / Crofts, A.R. / Nair, S.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2nvf.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2nvf.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/2nvf ftp://data.pdbj.org/pub/pdb/validation_reports/nv/2nvf | HTTPS FTP |
---|
-Related structure data
Related structure data | 2nukSC 2numC 2nveC 2nvgC 2nwfC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15178.206 Da / Num. of mol.: 1 / Fragment: residues 47-187 / Mutation: S154C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Production host: Escherichia coli (E. coli) / References: UniProt: Q02762, quinol-cytochrome-c reductase | ||
---|---|---|---|
#2: Chemical | ChemComp-FES / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
---|---|
Crystal grow | Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1.5 M ammonium sulfate, 20% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 276K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
---|---|
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→18 Å / Num. all: 21968 / Num. obs: 21968 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2188 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2NUK Resolution: 1.5→18 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.195 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.067 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.452 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.581 Å / Total num. of bins used: 10
|