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- PDB-7owy: 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: 7owy | ||||||
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Title | Crystal structure of human mitochondrial ferritin (hMTF) Fe(II)-loaded for 3 minutes showing a peroxide anion as bridging species of iron ions in the ferroxidase site | ||||||
![]() | Ferritin, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / human mitochondrial ferritin / hMTF / time-controlled iron loading / ferroxidase site / peroxide 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 | ![]() | 67.1 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o63C ![]() 7o64C ![]() 7o65C ![]() 7o66C ![]() 7o67C ![]() 7o68C ![]() 7o69C ![]() 7o6aC ![]() 7o6cC ![]() 7o6dC ![]() 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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1 | ![]()
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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, 358 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-PEO / | #4: Chemical | #5: Chemical | ChemComp-CL / #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: 3.16 Å3/Da / Density % sol: 61.07 % / 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2018 |
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→65.09 Å / Num. obs: 39259 / % possible obs: 100 % / Observed criterion σ(F): 2 / Redundancy: 21.2 % / Biso Wilson estimate: 10.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.036 / Rrim(I) all: 0.168 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 20.9 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 5609 / CC1/2: 0.929 / Rpim(I) all: 0.141 / Rrim(I) all: 0.646 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R03 Resolution: 1.55→55.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.964 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.063 / 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: 58.22 Å2 / Biso mean: 15.044 Å2 / Biso min: 4.19 Å2
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Refine analyze | Luzzati coordinate error obs: 0.137 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→55.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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