+Open data
-Basic information
Entry | Database: PDB / ID: 4xkt | |||||||||
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Title | E coli BFR variant Y149F | |||||||||
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 / 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: 1.82 Å | |||||||||
Authors | Bradley, J.M. / Hemmings, A.M. / Le Brun, N.E. | |||||||||
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 | 4xkt.cif.gz | 853.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xkt.ent.gz | 713.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xkt_validation.pdf.gz | 517.3 KB | Display | wwPDB validaton report |
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Full document | 4xkt_full_validation.pdf.gz | 534.8 KB | Display | |
Data in XML | 4xkt_validation.xml.gz | 99.6 KB | Display | |
Data in CIF | 4xkt_validation.cif.gz | 147.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/4xkt ftp://data.pdbj.org/pub/pdb/validation_reports/xk/4xkt | HTTPS FTP |
-Related structure data
Related structure data | 4xksC 4xkuC 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: Y149F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: bfr, BN1008_2995, BN17_32701, BU34_11470, BU65_02845, BU66_00425, BU67_22375, BU68_21080, BU69_14600, CF57_02675, CF61_03435, DO98_13405, DP79_03550, ECHMS174_03989, ECRV308_03369, EH62_04010, ...Gene: bfr, BN1008_2995, BN17_32701, BU34_11470, BU65_02845, BU66_00425, BU67_22375, BU68_21080, BU69_14600, CF57_02675, CF61_03435, DO98_13405, DP79_03550, ECHMS174_03989, ECRV308_03369, EH62_04010, EH63_09485, EH64_04335, EH65_17065, EH66_25435, EL75_0360, EL77_0399, EL78_0411, EL79_0379, EL80_0371, EP08_09090, GR02_14320, GR05_21335, GR06_21735, KV39_17170, LF82_0224, PGD_00550 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: E2QFJ1, UniProt: P0ABD3*PLUS, 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: 3.5 Å3/Da / Density % sol: 64.83 % |
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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 / Wavelength: 0.92 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→31.745 Å / Num. obs: 277740 / % possible obs: 99.8 % / Redundancy: 27 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 27.4 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 5.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2y3q Resolution: 1.82→31.745 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.39 / 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: 1.82→31.745 Å
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Refine LS restraints |
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LS refinement shell |
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