+Open data
-Basic information
Entry | Database: PDB / ID: 5z8j | |||||||||
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Title | Human mitochondrial ferritin mutant - E27C/E62C/C102G/C130G | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Zang, J. / Zheng, B. / Zhao, G. | |||||||||
Funding support | China, 2items
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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 | 5z8j.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z8j.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z8j_validation.pdf.gz | 424.3 KB | Display | wwPDB validaton report |
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Full document | 5z8j_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | 5z8j_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 5z8j_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/5z8j ftp://data.pdbj.org/pub/pdb/validation_reports/z8/5z8j | HTTPS FTP |
-Related structure data
Related structure data | 5z8sC 5z8uC 5z91C 1r03S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 20832.246 Da / Num. of mol.: 1 / Mutation: E27C/E62C/C102G/C130G 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 | ChemComp-AU / |
#3: 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: 3.05 Å3/Da / Density % sol: 59.63 % |
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Crystal grow | Temperature: 297 K / Method: evaporation / pH: 8.5 / Details: 3.4M 1,6-Hexanediol, 0.1M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 80 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: 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: 2.3→41.904 Å / Num. obs: 12124 / % possible obs: 100 % / Redundancy: 6.5 % / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.3→2.383 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R03 Resolution: 2.3→41.904 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→41.904 Å
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Refine LS restraints |
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LS refinement shell |
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