+Open data
-Basic information
Entry | Database: PDB / ID: 4y08 | ||||||
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Title | ONE MINUTE IRON LOADED HUMAN H FERRITIN | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / ferroxidase / Ferritin heavy chain / iron homeostasis | ||||||
Function / homology | Function and homology information 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 / 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: 1.34 Å | ||||||
Authors | Pozzi, C. / Di Pisa, F. / Mangani, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Iron binding to human heavy-chain ferritin. Authors: Pozzi, C. / Di Pisa, F. / Bernacchioni, C. / Ciambellotti, S. / Turano, P. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y08.cif.gz | 64.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y08.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 4y08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/4y08 ftp://data.pdbj.org/pub/pdb/validation_reports/y0/4y08 | HTTPS FTP |
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-Related structure data
Related structure data | 4oynC 4ykhC 4zjkC 3ajoS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21255.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Plasmid: pET9A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02794, ferroxidase |
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-Non-polymers , 5 types, 349 molecules
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.09 % / Description: bipyramidal crystals |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.0 M magnesium chloride and 0.1 M BICINE at pH 9.0 PH range: 7.7 - 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→29.11 Å / Num. all: 60022 / Num. obs: 60022 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 20 % / Biso Wilson estimate: 8.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 1.34→1.41 Å / Redundancy: 20 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AJO Resolution: 1.34→27.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.543 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: shapes of electron density closed to Fe2 and Fe3 are compatible with Oxygen but there is no experimental evidence of its presence.
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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 mean: 12.024 Å2
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Refinement step | Cycle: 1 / Resolution: 1.34→27.76 Å
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Refine LS restraints |
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