+Open data
-Basic information
Entry | Database: PDB / ID: 5z91 | ||||||
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Title | Human mitochondrial ferritin mutant bound with gold ions | ||||||
Components | Ferritin, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Human mitochondrial ferritin / gold / cysteine / METAL BINDING PROTEIN | ||||||
Function / homology | Function and homology information positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / positive regulation of aconitate hydratase activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport ...positive regulation of lyase activity / positive regulation of succinate dehydrogenase activity / positive regulation of aconitate hydratase activity / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / Iron uptake and transport / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / mitochondrial matrix / iron ion binding / positive regulation of cell population proliferation / mitochondrion / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.004 Å | ||||||
Authors | Zang, J. / Zheng, B. / Zhao, G. | ||||||
Funding support | China, 1items
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Citation | Journal: J Nanobiotechnology / Year: 2019 Title: Design and site-directed compartmentalization of gold nanoclusters within the intrasubunit interfaces of ferritin nanocage. Authors: Zang, J. / Zheng, B. / Zhang, X. / Arosio, P. / Zhao, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z91.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z91.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z91_validation.pdf.gz | 420.3 KB | Display | wwPDB validaton report |
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Full document | 5z91_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 5z91_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 5z91_validation.cif.gz | 11 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/5z91 ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z91 | HTTPS FTP |
-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: 20976.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTMT / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N4E7, ferroxidase | ||||
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#2: Chemical | #3: Chemical | #4: 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 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: Bicine, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3→45.52 Å / Num. obs: 5579 / % possible obs: 100 % / Redundancy: 16.1 % / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 3→3.11 Å |
-Processing
Software |
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Refinement | Resolution: 3.004→45.52 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.004→45.52 Å
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Refine LS restraints |
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LS refinement shell |
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