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- PDB-5vtd: Crystal Structure of the Co-bound Human Heavy-Chain Ferritin vari... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vtd | ||||||
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Title | Crystal Structure of the Co-bound Human Heavy-Chain Ferritin variant 122H-delta C-star | ||||||
![]() | Ferritin heavy chain | ||||||
![]() | OXIDOREDUCTASE / Node / Maxi-ferritin | ||||||
Function / homology | ![]() iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / ferritin complex / negative regulation of ferroptosis / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / autolysosome / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding / autophagosome / 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 / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bailey, J.B. / Zhang, L. / Chiong, J.A. / Tezcan, F.A. | ||||||
![]() | ![]() Title: Synthetic Modularity of Protein-Metal-Organic Frameworks. Authors: Bailey, J.B. / Zhang, L. / Chiong, J.A. / Ahn, S. / Tezcan, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.2 KB | Display | ![]() |
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PDB format | ![]() | 42.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.8 KB | Display | ![]() |
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Full document | ![]() | 414.7 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5up7C ![]() 5up8C ![]() 5up9C ![]() 5cmqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 21122.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.44 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Reservoir: 500 uL total volume: 25 mM Tris (pH 8), 12 mM CaCl2, 150 mM NaCl, 0.3 mM CoCl2, 1% PEG 1900 MME Sitting Drop: 2 uL reservoir, 2 uL of 4 uM ferritin |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: APEX II CCD / Detector: CCD / Date: May 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→63.72 Å / Num. obs: 18852 / % possible obs: 99.5 % / Redundancy: 8.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.95→2.03 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2 / CC1/2: 0.797 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CMQ Resolution: 1.95→63.72 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.95→63.72 Å
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