+Open data
-Basic information
Entry | Database: PDB / ID: 3ajp | ||||||
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Title | Crystal structure of human H ferritin E140A mutant | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / 4-helix bundle | ||||||
Function / homology | Function and homology information iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / ferrous iron binding / Iron uptake and transport / tertiary granule lumen / iron ion transport / intracellular iron ion homeostasis / ficolin-1-rich granule lumen / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Masuda, T. / Mikami, B. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ajp.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ajp.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ajp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/3ajp ftp://data.pdbj.org/pub/pdb/validation_reports/aj/3ajp | HTTPS FTP |
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-Related 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: 21066.424 Da / Num. of mol.: 1 / Mutation: E140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02794, ferroxidase | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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