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- PDB-5up9: Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5up9 | ||||||
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Title | Crystal Structure of Zn-bound Human Heavy-Chain ferritin variant 122H-delta C-star with para-xylenedihydroxamate | ||||||
![]() | Ferritin heavy chain | ||||||
![]() | OXIDOREDUCTASE / oxidoreductase self-assembly Protein-MOF Protein-Metal-Organic Framework | ||||||
Function / homology | ![]() iron ion sequestering activity / : / negative regulation of ferroptosis / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation ...iron ion sequestering activity / : / negative regulation of ferroptosis / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bailey, J.B. / Zhang, L. / Chiong, J.A. / Ahn, S. / 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 | ![]() | 262.1 KB | Display | ![]() |
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PDB format | ![]() | 213.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5up7C ![]() 5up8C ![]() 5vtdC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: (Selection details: (chain F and (resseq 5:48 or (resid 49 and (name...) |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 21122.291 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1138 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BYX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/BYX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-BYX / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 8.5), 150 mM NaCl, 0.474 mM ZnCl2, 3% PEG 300 Sitting Drop: 7.6 uL reservoir, 2 uL of 12.5 uM ferritin, 2.4 uL of 5 mM p-H2xdh in 50 mM CHES ...Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 8.5), 150 mM NaCl, 0.474 mM ZnCl2, 3% PEG 300 Sitting Drop: 7.6 uL reservoir, 2 uL of 12.5 uM ferritin, 2.4 uL of 5 mM p-H2xdh in 50 mM CHES (pH 9.5) with 150 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→47.397 Å / Num. obs: 64992 / % possible obs: 99.1 % / Redundancy: 5.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.139 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6201 / CC1/2: 0.945 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CMQ Resolution: 2.45→47.4 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 2.45→47.4 Å
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LS refinement shell | Resolution: 2.4507→2.4873 Å
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