+Open data
-Basic information
Entry | Database: PDB / ID: 4zjk | ||||||
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Title | FIVE MINUTES IRON LOADED HUMAN H FERRITIN | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / Iron Storage Protein | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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 | 4zjk.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zjk.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 4zjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zjk_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
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Full document | 4zjk_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 4zjk_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 4zjk_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zjk ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zjk | HTTPS FTP |
-Related structure data
Related structure data | 4oynC 4y08C 4ykhC 3ajoS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 21124.459 Da / Num. of mol.: 1 / Fragment: UNP residues 2-183 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTH1, FTH, FTHL6, OK/SW-cl.84, PIG15 / Plasmid: pET-9a / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P02794, ferroxidase | ||||||
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#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.83 % / Description: Cubic Crystals |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 Bicine pH 9.0, 2.0 M Magnesium Chloride / PH range: 7.5-9 |
-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 6, 2013 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→31.07 Å / Num. obs: 38257 / % possible obs: 99.8 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.059 / Rsym value: 0.023 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.56→1.64 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.6 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AJO Resolution: 1.56→31.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.181 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 15.845 Å2
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Refinement step | Cycle: 1 / Resolution: 1.56→31.07 Å
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