+Open data
-Basic information
Entry | Database: PDB / ID: 5ouw | ||||||
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Title | Metal free structure of SynFtn | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / Ferritin | ||||||
Function / homology | Function and homology information bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | Synechococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Hemmings, A.M. / Bradley, J.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Reaction of O2with a diiron protein generates a mixed-valent Fe2+/Fe3+center and peroxide. Authors: Bradley, J.M. / Svistunenko, D.A. / Pullin, J. / Hill, N. / Stuart, R.K. / Palenik, B. / Wilson, M.T. / 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 | 5ouw.cif.gz | 86.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ouw.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ouw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/5ouw ftp://data.pdbj.org/pub/pdb/validation_reports/ou/5ouw | HTTPS FTP |
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-Related structure data
Related structure data | 5ouzC 6gkaC 6gkbC 6gkcC 1eumS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19756.840 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria) Strain: CC9311 / Gene: sync_1539 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0I9X8, bacterial non-heme ferritin |
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#2: 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: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: ammonium acetate, sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→53.59 Å / Num. obs: 15595 / % possible obs: 99.7 % / Redundancy: 54.9 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.01 / Rrim(I) all: 0.075 / Net I/σ(I): 53.2 |
Reflection shell | Resolution: 2.05→2.1 Å / Rmerge(I) obs: 0.644 / CC1/2: 0.986 / Rpim(I) all: 0.085 / Rrim(I) all: 0.649 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EUM Resolution: 2.05→53.591 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.7 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.23 Å2 / Biso mean: 31.8214 Å2 / Biso min: 16.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→53.591 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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