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Yorodumi- PDB-7o66: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o66 | ||||||
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Title | Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 60 minutes showing either a dioxygen or a superoxide anion coordinated to iron ions in the ferroxidase site | ||||||
Components | Ferritin, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site / dioxygen / superoxide anion | ||||||
Function / homology | Function and homology information positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / positive regulation of aconitate hydratase activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport ...positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / positive regulation of aconitate hydratase activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / mitochondrial matrix / iron ion binding / positive regulation of cell population proliferation / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Pozzi, C. / Ciambellotti, S. / Tassone, G. / Turano, P. / Mangani, S. | ||||||
Citation | Journal: Chemistry / Year: 2021 Title: Iron Binding in the Ferroxidase Site of Human Mitochondrial Ferritin. Authors: Ciambellotti, S. / Pratesi, A. / Tassone, G. / Turano, P. / Mangani, S. / Pozzi, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o66.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o66.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 7o66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o66_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 7o66_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 7o66_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7o66_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/7o66 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/7o66 | HTTPS FTP |
-Related structure data
Related structure data | 7o63C 7o64C 7o65C 7o67C 7o68C 7o69C 7o6aC 7o6cC 7o6dC 7owyC 1r03S 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21107.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTMT / Plasmid: pET-3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pLysS / References: UniProt: Q8N4E7, ferroxidase |
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-Non-polymers , 5 types, 314 molecules
#2: Chemical | ChemComp-OXY / | ||||||
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#3: Chemical | ChemComp-FE2 / #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % / Description: Octahedral crystals |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 1.6-2 M MgCl2 6H2O and 0.1 M bicine pH 9.0 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 7O66 / Observed criterion σ(F): 2
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Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R03 Resolution: 1.6→64.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.207 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.31 Å2 / Biso mean: 22.355 Å2 / Biso min: 12.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.144 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→64.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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