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Yorodumi- PDB-7ck8: Crystal structure of human ferritin heavy chain mutant C90S/C102S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ck8 | |||||||||||||||
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Title | Crystal structure of human ferritin heavy chain mutant C90S/C102S/C130S | |||||||||||||||
Components | Ferritin heavy chain | |||||||||||||||
Keywords | METAL TRANSPORT / iron storage / ferroxidase activity / nancage | |||||||||||||||
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 / AB INITIO PHASING / Resolution: 1.8 Å | |||||||||||||||
Authors | Chen, X. / Jiang, B. / Yan, X. / Fan, K. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Nano Today / Year: 2020 Title: A natural drug entry channel in the ferritin nanocage. Authors: Jiang, B. / Chen, X. / Sun, G. / Chen, X. / Yin, Y. / Jin, Y. / Mi, Q. / Ma, L. / Yang, Y. / Yan, X. / Fan, K. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ck8.cif.gz | 553.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ck8.ent.gz | 453.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ck8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ck8 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ck8 | HTTPS FTP |
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-Related structure data
-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
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 20155.428 Da / Num. of mol.: 12 / Mutation: C90S, C102S, C130S 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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-Non-polymers , 6 types, 3489 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-OXY / #6: Chemical | ChemComp-FE / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.17 Å3/Da / Density % sol: 61.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 0.1 M Bicine, pH 9.0, 1.7-2.0 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97905 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→30 Å / Num. obs: 333244 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.39 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.143 / Χ2: 1.398 / Net I/av σ(I): 10.34 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.8→28.976 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.28 / Stereochemistry target values: ML Details: 1. bulk solvent correction 2. refinement of coordinates 3. refinement of ADPs 4. refinement of occupancies
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.5 Å2 / Biso mean: 19.7966 Å2 / Biso min: 9.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→28.976 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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