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Yorodumi- PDB-7o63: High resolution crystal structure of human mitochondrial ferritin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o63 | ||||||
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Title | High resolution crystal structure of human mitochondrial ferritin (hMTF) | ||||||
Components | Ferritin, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / human mitochondrial ferritin / hMTF / high resolution | ||||||
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: 1.16 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 | 7o63.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o63.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 7o63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o63_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
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Full document | 7o63_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 7o63_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 7o63_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/7o63 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/7o63 | HTTPS FTP |
-Related structure data
Related structure data | 7o64C 7o65C 7o66C 7o67C 7o68C 7o69C 7o6aC 7o6cC 7o6dC 7owyC 1r03S 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: 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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#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.09 % / 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 | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→65.1 Å / Num. obs: 92014 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Redundancy: 20.2 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.03 / Rrim(I) all: 0.098 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.16→1.22 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 13215 / CC1/2: 0.855 / Rpim(I) all: 0.2 / Rrim(I) all: 0.76 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R03 Resolution: 1.16→65.1 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.63 / SU ML: 0.015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 78.26 Å2 / Biso mean: 12.785 Å2 / Biso min: 6.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1156 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.16→65.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.16→1.19 Å / Rfactor Rfree error: 0
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