+Open data
-Basic information
Entry | Database: PDB / ID: 4xku | |||||||||
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Title | E coli BFR variant Y114F | |||||||||
Components | Bacterioferritin | |||||||||
Keywords | METAL BINDING PROTEIN / Iron Storage / diiron site | |||||||||
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: 1.78 Å | |||||||||
Authors | Hemmings, A.M. / Le Brun, N.E. / Bradley, J.M. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Three Aromatic Residues are Required for Electron Transfer during Iron Mineralization in Bacterioferritin. Authors: Bradley, J.M. / Svistunenko, D.A. / Lawson, T.L. / Hemmings, A.M. / Moore, G.R. / Le Brun, N.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xku.cif.gz | 463.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xku.ent.gz | 381.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xku_validation.pdf.gz | 516 KB | Display | wwPDB validaton report |
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Full document | 4xku_full_validation.pdf.gz | 527.7 KB | Display | |
Data in XML | 4xku_validation.xml.gz | 99.4 KB | Display | |
Data in CIF | 4xku_validation.cif.gz | 149.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xku ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xku | HTTPS FTP |
-Related structure data
Related structure data | 4xksC 4xktC 2y3qS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18502.016 Da / Num. of mol.: 12 / Mutation: Y114F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: bfr, b3336, JW3298 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABD3, ferroxidase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1.6M ammonium sulfate 0.1M sodium citrate / PH range: 4.8-5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→102.271 Å / Num. obs: 287797 / % possible obs: 96.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.78→1.83 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.5 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y3Q Resolution: 1.78→102.271 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→102.271 Å
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Refine LS restraints |
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LS refinement shell |
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