+Open data
-Basic information
Entry | Database: PDB / ID: 5z8s | ||||||
---|---|---|---|---|---|---|---|
Title | Human Mitochondrial ferritin mutant - C102A/C130A/E27C/E61C/E62C | ||||||
Components | Ferritin, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Mitochondrail 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: 1.973 Å | ||||||
Authors | Zang, J. / Zheng, B. / Zhao, G. | ||||||
Funding support | China, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5z8s.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5z8s.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 5z8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z8s_validation.pdf.gz | 411.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5z8s_full_validation.pdf.gz | 411.2 KB | Display | |
Data in XML | 5z8s_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5z8s_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/5z8s ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z8s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20806.273 Da / Num. of mol.: 1 / Mutation: E27C/E61C/E62C/C102A/C130A 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 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / Details: 0.1M Tris-HCl, 3.4M 1,6-Hexanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 27, 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: 1.973→41.923 Å / Num. obs: 18997 / % possible obs: 100 % / Redundancy: 12.3 % / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.973→2.044 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.973→41.923 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.72
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.973→41.923 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|