+Open data
-Basic information
Entry | Database: PDB / ID: 6ipp | ||||||
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Title | Non-native ferritin 8-mer mutant-C90A/C102A/C130A/D144C | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / ferritin / cysteine | ||||||
Function / homology | Function and homology information 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.699 Å | ||||||
Authors | Zang, J. / Chen, H. / Zhou, K. / Zhao, G. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Disulfide-mediated conversion of 8-mer bowl-like protein architecture into three different nanocages. Authors: Zang, J. / Chen, H. / Zhang, X. / Zhang, C. / Guo, J. / Du, M. / Zhao, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ipp.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ipp.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ipp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ipp_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 6ipp_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 6ipp_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 6ipp_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ip/6ipp ftp://data.pdbj.org/pub/pdb/validation_reports/ip/6ipp | HTTPS FTP |
-Related structure data
Related structure data | 6ipcC 6ipoC 6ipqC 6j7gC 2fhaS 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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Unit cell |
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-Components
#1: Protein | Mass: 20345.584 Da / Num. of mol.: 2 / Mutation: C90A/C102A/C130A/D144C 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 #2: Chemical | ChemComp-FE / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 293.17 K / Method: evaporation / pH: 7 / Details: Sodium chloride,MPD,TRIS |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9779 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 2.699→48.05 Å / Num. obs: 15943 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 1 / Rmerge(I) obs: 0.1944 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.699→3.105 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FHA Resolution: 2.699→48.046 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 21.81
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.699→48.046 Å
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Refine LS restraints |
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LS refinement shell |
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