+Open data
-Basic information
Entry | Database: PDB / ID: 5znd | ||||||
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Title | 8-mer nanotube derived from 24-mer rHuHF nanocage | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | METAL BINDING PROTEIN / Ferritin / rHuHF / protein redesign / nanotube | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Wang, W.M. / Wang, L.L. / Zang, J.C. / Chen, H. / Zhao, G.H. / Wang, H.F. | ||||||
Funding support | China, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Selective Elimination of the Key Subunit Interfaces Facilitates Conversion of Native 24-mer Protein Nanocage into 8-mer Nanorings. Authors: Wang, W. / Wang, L. / Chen, H. / Zang, J. / Zhao, X. / Zhao, G. / Wang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5znd.cif.gz | 38.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5znd.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 5znd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/5znd ftp://data.pdbj.org/pub/pdb/validation_reports/zn/5znd | HTTPS FTP |
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-Related structure data
Related structure data | 2fhaS S: Starting model for refinement |
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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: 15762.584 Da / Num. of mol.: 1 / Mutation: K86Q 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: 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: 2.06 Å3/Da / Density % sol: 40.43 % / Description: needle like |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M ammonium citrate (pH=8.0), 0.1M Tris-HCl (pH=8.0), 22% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9779 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 2, 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: 3→50 Å / Num. obs: 2556 / % possible obs: 90.1 % / Redundancy: 11.5 % / CC1/2: 0.982 / Rmerge(I) obs: 0.117 / Rrim(I) all: 0.124 / Net I/σ(I): 19.58 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 6.15 / Num. unique obs: 134 / CC1/2: 0.96 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FHA Resolution: 3→33.894 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→33.894 Å
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Refine LS restraints |
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LS refinement shell |
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