+Open data
-Basic information
Entry | Database: PDB / ID: 8w92 | ||||||
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Title | human H ferritin with 2 Fe(II)/subunit loading | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | METAL BINDING PROTEIN / enzyme | ||||||
Function / homology | Function and homology information iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / autophagosome / 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 / immune response / iron ion binding / negative regulation of cell population proliferation / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Zhang, T. / Jiao, R. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: human H ferritin with 2 Fe(II)/subunit loading Authors: Zhang, T. / Jiao, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w92.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w92.ent.gz | 38.3 KB | Display | PDB format |
PDBx/mmJSON format | 8w92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w92_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8w92_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8w92_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 8w92_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/8w92 ftp://data.pdbj.org/pub/pdb/validation_reports/w9/8w92 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 21254.605 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P02794, ferroxidase | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES, pH7, 20 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 1.6314 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6314 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→37.2 Å / Num. obs: 15266 / % possible obs: 99.9 % / Redundancy: 28 % / CC1/2: 1 / Net I/σ(I): 31.86 |
Reflection shell | Resolution: 2.121→2.196 Å / Num. unique obs: 1491 / CC1/2: 0.832 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→37.2 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→37.2 Å
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Refine LS restraints |
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LS refinement shell |
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