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- PDB-7o68: Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o68 | ||||||
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Title | Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 120 minutes showing either a dioxygen or a superoxide anion coordinated to iron ions in the ferroxidase site. | ||||||
![]() | Ferritin, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site / dioxygen / superoxide anion | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozzi, C. / Ciambellotti, S. / Tassone, G. / Turano, P. / Mangani, S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.6 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.5 KB | Display | ![]() |
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Full document | ![]() | 382.5 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o63C ![]() 7o64C ![]() 7o65C ![]() 7o66C ![]() 7o67C ![]() 7o69C ![]() 7o6aC ![]() 7o6cC ![]() 7o6dC ![]() 7owyC ![]() 1r03S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 327 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-OXY / | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.29 % / 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: 7O68 / Observed criterion σ(F): 2 / % possible obs: 100 %
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Reflection shell | % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R03 Resolution: 1.68→64.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.374 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08 / 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: 68.58 Å2 / Biso mean: 18.016 Å2 / Biso min: 8.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1505 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→64.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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