+Open data
-Basic information
Entry | Database: PDB / ID: 4cvp | ||||||
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Title | Structure of Apobacterioferritin | ||||||
Components | BACTERIOFERRITIN | ||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / oxidoreductase activity / iron ion binding / heme binding / protein homodimerization activity ...ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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: 2.11 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cvp.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvp.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cvp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cvp_validation.pdf.gz | 425.9 KB | Display | wwPDB validaton report |
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Full document | 4cvp_full_validation.pdf.gz | 426.3 KB | Display | |
Data in XML | 4cvp_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 4cvp_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvp ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvp | HTTPS FTP |
-Related structure data
Related structure data | 4cvrC 4cvsC 4cvtC 2vxiS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 18627.188 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: P0ABD4, UniProt: P0ABD3*PLUS, ferroxidase | ||
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#2: Chemical | #3: 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: 1.93 Å3/Da / Density % sol: 36.3 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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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: 2.1→46.66 Å / Num. obs: 8475 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.16 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.81 / % possible all: 99.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VXI Resolution: 2.11→46.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.879 / SU B: 12.843 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 37.524 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→46.64 Å
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Refine LS restraints |
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