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Yorodumi- PDB-8j9l: Crystal Structure of Human H-Ferritin variant 123F assembling in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j9l | ||||||
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Title | Crystal Structure of Human H-Ferritin variant 123F assembling in solution2 | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / protein assembly | ||||||
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: 2.5 Å | ||||||
Authors | Chen, X. / Zhao, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Adv Sci / Year: 2023 Title: Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular pi-pi Interactions. Authors: Chen, X. / Zhang, T. / Liu, H. / Zang, J. / Lv, C. / Du, M. / Zhao, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j9l.cif.gz | 412.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j9l.ent.gz | 340.3 KB | Display | PDB format |
PDBx/mmJSON format | 8j9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j9l_validation.pdf.gz | 6.2 MB | Display | wwPDB validaton report |
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Full document | 8j9l_full_validation.pdf.gz | 6.2 MB | Display | |
Data in XML | 8j9l_validation.xml.gz | 67.1 KB | Display | |
Data in CIF | 8j9l_validation.cif.gz | 92.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/8j9l ftp://data.pdbj.org/pub/pdb/validation_reports/j9/8j9l | HTTPS FTP |
-Related structure data
Related structure data | 8j9mC 8jaiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21287.742 Da / Num. of mol.: 12 / Mutation: D123F 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 #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.13 Å3/Da / Density % sol: 70.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: 50 mM BICINE pH 9.5, 800 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.26 Å / Num. obs: 144447 / % possible obs: 97.24 % / Redundancy: 2 % / CC1/2: 0.412 / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 14354 / CC1/2: 0.702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.26 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.06 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.26 Å
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Refine LS restraints |
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LS refinement shell |
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