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Yorodumi- PDB-7jgo: Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jgo | ||||||
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Title | Crystal Structure of the Ni-bound Human Heavy-chain variant 122H-delta C-star with 2,5-furandihyrdoxamate collected at 278K | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / Protein-MOF / Ferritin-MOF / Self-Assembly / Ferritin | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.08 Å | ||||||
Authors | Bailey, J.B. / Tezcan, F.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Tunable and Cooperative Thermomechanical Properties of Protein-Metal-Organic Frameworks. Authors: Bailey, J.B. / Tezcan, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jgo.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jgo.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/7jgo ftp://data.pdbj.org/pub/pdb/validation_reports/jg/7jgo | HTTPS FTP |
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-Related structure data
Related structure data | 7jgkC 7jglC 7jgmC 7jgnC 7jgpC 7jgqC 5cmqS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21122.291 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 | ChemComp-V9Y / | ||||||
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: 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: 3.75 Å3/Da / Density % sol: 67.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 9.5), 150 mM NaCl, 0.474 mM NiCl2, 12.6% PEP Sitting Drop: 12.7 uL reservoir, 3.3 uL of 25 uM ferritin, 4 uL of 10 mM fdh in 50 mM CHES (pH 9.5) with 150 mM NaCl |
-Data collection
Diffraction | Mean temperature: 278 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Sep 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 3.08→49.36 Å / Num. obs: 11398 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 48.66 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.08→3.19 Å / Num. unique obs: 1026 / CC1/2: 0.899 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CMQ Resolution: 3.08→49.36 Å / SU ML: 0.359 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.3106 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 39.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.08→49.36 Å
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Refine LS restraints |
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LS refinement shell |
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