+Open data
-Basic information
Entry | Database: PDB / ID: 6gka | ||||||
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Title | 20 minute Fe2+ soak structure of SynFtn | ||||||
Components | Ferritin | ||||||
Keywords | METAL BINDING PROTEIN / Ferritin | ||||||
Function / homology | Function and homology information bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytosol Similarity search - Function | ||||||
Biological species | Synechococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.76 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 | 6gka.cif.gz | 89.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gka.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gka_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6gka_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6gka_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 6gka_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/6gka ftp://data.pdbj.org/pub/pdb/validation_reports/gk/6gka | HTTPS FTP |
-Related structure data
Related structure data | 5ouwC 5ouzC 6gkbC 6gkcC 5ouv 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: 19813.893 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: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.93 Å3/Da / Density % sol: 57.99 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate 2.0 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97953 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.76→53.45 Å / Num. obs: 23392 / % possible obs: 97.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Net I/σ(I): 15.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 1.76→40.666 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.02 Å2 / Biso mean: 28.6336 Å2 / Biso min: 16.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.76→40.666 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: 28.6083 Å / Origin y: -10.3594 Å / Origin z: -37.8779 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 5 through 182) |