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Yorodumi- PDB-5j93: Five minutes iron loaded Rana Catesbeiana H' ferritin variant E57... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j93 | ||||||
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Title | Five minutes iron loaded Rana Catesbeiana H' ferritin variant E57A/E136A/D140A | ||||||
Components | Ferritin, middle subunit | ||||||
Keywords | OXIDOREDUCTASE / Rana Catesbeiana / ferritin variant / ferroxidase activity / M type / H' type / oxidoreductase activity / iron | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | ||||||
Biological species | Lithobates catesbeiana (American bullfrog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Pozzi, C. / Di Pisa, F. / Mangani, S. / Bernacchioni, C. / Turano, P. | ||||||
Citation | Journal: Chemistry / Year: 2016 Title: Ferroxidase Activity in Eukaryotic Ferritin is Controlled by Accessory-Iron-Binding Sites in the Catalytic Cavity. Authors: Bernacchioni, C. / Pozzi, C. / Di Pisa, F. / Mangani, S. / Turano, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j93.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j93.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 5j93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5j93_validation.pdf.gz | 422.2 KB | Display | wwPDB validaton report |
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Full document | 5j93_full_validation.pdf.gz | 422.9 KB | Display | |
Data in XML | 5j93_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 5j93_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/5j93 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/5j93 | HTTPS FTP |
-Related structure data
Related structure data | 5j8sSC 5j8wC 5j9vC 5jacC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20463.100 Da / Num. of mol.: 1 / Mutation: E57A, E136A, D140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates catesbeiana (American bullfrog) Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P07798, ferroxidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / #5: 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: 3.27 Å3/Da / Density % sol: 62.4 % / Description: Octahedral crystals |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.000, 1.722, 1.759 | ||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2014 | ||||||||||||
Radiation | Monochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.1→45.95 Å / Num. obs: 104724 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.1 | ||||||||||||
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.5 / % possible all: 84.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J8S Resolution: 1.1→45.95 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / Rfactor Rfree error: 0.022 / SU B: 0.577 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.965 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→45.95 Å
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Refine LS restraints |
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