+Open data
-Basic information
Entry | Database: PDB / ID: 4cvt | ||||||
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Title | Structure of Apobacterioferritin Y58F variant | ||||||
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 / 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: 1.794 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 | 4cvt.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cvt.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 4cvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cvt_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 4cvt_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 4cvt_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4cvt_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/4cvt ftp://data.pdbj.org/pub/pdb/validation_reports/cv/4cvt | HTTPS FTP |
-Related structure data
Related structure data | 4cvpC 4cvrC 4cvsC 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: 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 | ||||
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#2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | N-TERMINAL ALA AS CLONING ARTEFACT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.04 % / 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: 1.41→46.82 Å / Num. obs: 13671 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.11 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.39 |
Reflection shell | Resolution: 1.79→1.84 Å / Redundancy: 3.03 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.31 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VXI Resolution: 1.794→46.817 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.132 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.326 Å2
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Refinement step | Cycle: LAST / Resolution: 1.794→46.817 Å
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Refine LS restraints |
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