+Open data
-Basic information
Entry | Database: PDB / ID: 4cvs | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Apobacterioferritin Y45F variant | ||||||
Components | BACTERIOFERRITIN | ||||||
Keywords | OXIDOREDUCTASE / FERRITIN / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding ...ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.392 Å | ||||||
Authors | Hingorani, K. / Pace, R. / Whitney, S. / Murray, J.W. / Wydrzynski, T. / Cheah, M.H. / Smith, P. / Hillier, W. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Photo-Oxidation of Tyrosine in a Bio-Engineered Bacterioferritin 'Reaction Centre'-A Protein Model for Artificial Photosynthesis. Authors: Hingorani, K. / Pace, R. / Whitney, S. / Murray, J.W. / Smith, P. / Cheah, M.H. / Wydrzynski, T. / Hillier, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cvs.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cvs.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 4cvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cvs_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cvs_full_validation.pdf.gz | 428.3 KB | Display | |
Data in XML | 4cvs_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4cvs_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvs ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvs | HTTPS FTP |
-Related structure data
Related structure data | 4cvpC 4cvrC 4cvtC 2vxiS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 18611.188 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ABD3, ferroxidase | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.87 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0077 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 5, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0077 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→49.56 Å / Num. obs: 26385 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.32 |
Reflection shell | Resolution: 1.39→1.4 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.02 / % possible all: 74.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VXI Resolution: 1.392→49.557 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.915 / SU B: 1.432 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.712 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.392→49.557 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|