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Yorodumi- PDB-5up8: Crystal Structure of the Zn-bound Human Heavy-Chain variant 122H-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5up8 | ||||||
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Title | Crystal Structure of the Zn-bound Human Heavy-Chain variant 122H-delta C-star with para-benzenedihydroxamate | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / self-assembly / protein-MOF / protein-metal-organic framework | ||||||
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 / Resolution: 2.631 Å | ||||||
Authors | Bailey, J.B. / Zhang, L. / Chiong, J.C. / Ahn, S. / Tezcan, F.A. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5up8.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5up8.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 5up8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/5up8 ftp://data.pdbj.org/pub/pdb/validation_reports/up/5up8 | 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
#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 | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-BYD / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: Reservoir: 500 uL total volume: 50 mM CHES (pH 8.5), 150 mM NaCl, 0.14 mM ZnCl2 Sitting Drop: 8.6 uL reservoir, 1 uL of 12.5 uM ferritin, 2.4 uL of 5 mM p-H2bdh 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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→49.27 Å / Num. obs: 9926 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.63→2.75 Å / Redundancy: 23 % / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1189 / CC1/2: 0.554 / % possible all: 100 |
-Processing
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Refinement | Resolution: 2.631→49.27 Å / Cross valid method: THROUGHOUT / σ(Fsqd): 1.35 / Phase error: 28.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.87 Å2 / Biso mean: 84.5949 Å2 / Biso min: 47.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.631→49.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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