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Open data
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Basic information
Entry | Database: PDB / ID: 3ajp | ||||||
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Title | Crystal structure of human H ferritin E140A mutant | ||||||
![]() | Ferritin heavy chain | ||||||
![]() | OXIDOREDUCTASE / 4-helix bundle | ||||||
Function / homology | ![]() iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / Iron uptake and transport / ferrous iron binding / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / iron ion binding / immune response / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Masuda, T. / Mikami, B. | ||||||
![]() | ![]() Title: The universal mechanism for iron translocation to the ferroxidase site in ferritin, which is mediated by the well conserved transit site Authors: Masuda, T. / Goto, F. / Yoshihara, T. / Mikami, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.9 KB | Display | ![]() |
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PDB format | ![]() | 41.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.7 KB | Display | ![]() |
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Full document | ![]() | 426.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 21066.424 Da / Num. of mol.: 1 / Mutation: E140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.0M magnesium chloride, 0.1M Bicine (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 11, 2010 |
Radiation | Monochromator: Si double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 21234 / Num. obs: 21170 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 15.3 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 12.7 / Num. unique all: 2063 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Native human H ferritin Resolution: 1.901→30.496 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.912 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.465 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati sigma a obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→30.496 Å
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Refine LS restraints |
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LS refinement shell |
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