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Yorodumi- PDB-7urh: Crystal structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7urh | ||||||
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Title | Crystal structure of Ferritin 2 from Caenorhabditis elegans, FTN-2 | ||||||
Components | Ferritin | ||||||
Keywords | OXIDOREDUCTASE / Ferroxidase | ||||||
Function / homology | Function and homology information Iron uptake and transport / Neutrophil degranulation / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / defense response to Gram-positive bacterium / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.468 Å | ||||||
Authors | Malcolm, T.R. / Maher, M.J. / Mubarak, S.S.M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Biochemical Characterization of Caenorhabditis elegans Ferritins. Authors: Mubarak, S.S.M. / Malcolm, T.R. / Brown, H.G. / Hanssen, E. / Maher, M.J. / McColl, G. / Jameson, G.N.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7urh.cif.gz | 263.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7urh.ent.gz | 204.9 KB | Display | PDB format |
PDBx/mmJSON format | 7urh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7urh_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 7urh_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 7urh_validation.xml.gz | 51.8 KB | Display | |
Data in CIF | 7urh_validation.cif.gz | 78.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7urh ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7urh | HTTPS FTP |
-Related structure data
Related structure data | 7usnC 5wpnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19371.547 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ftn-2, CELE_D1037.3, D1037.3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9TYS3, ferroxidase #2: Chemical | ChemComp-FE / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 2-methyl-2,4-pentanediol, Bis-Tris, Ammonium acetate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 1.468→50 Å / Num. obs: 256649 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.47→1.49 Å / Rmerge(I) obs: 0.625 / Num. unique obs: 11916 / CC1/2: 0.847 / Rpim(I) all: 0.262 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WPN Resolution: 1.468→49.505 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.164 / SU B: 1.063 / SU ML: 0.039 / Average fsc free: 0.9362 / Average fsc work: 0.941 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.054 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.418 Å2
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Refinement step | Cycle: LAST / Resolution: 1.468→49.505 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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