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Yorodumi- PDB-5gou: Structure of a 16-mer protein nanocage fabricated from its 24-mer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gou | ||||||
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Title | Structure of a 16-mer protein nanocage fabricated from its 24-mer analogue by subunit interface redesign | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | OXIDOREDUCTASE / ferritin / 16-mer nanocage / subunit interface redesign | ||||||
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: 2.91 Å | ||||||
Authors | Zhang, S. / Zang, J. / Wang, W. / Wang, H. / Zhao, G. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2016 Title: Conversion of the Native 24-mer Ferritin Nanocage into Its Non-Native 16-mer Analogue by Insertion of Extra Amino Acid Residues. Authors: Zhang, S. / Zang, J. / Wang, W. / Chen, H. / Zhang, X. / Wang, F. / Wang, H. / Zhao, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gou.cif.gz | 901.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gou.ent.gz | 750.6 KB | Display | PDB format |
PDBx/mmJSON format | 5gou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/5gou ftp://data.pdbj.org/pub/pdb/validation_reports/go/5gou | 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
#1: Protein | Mass: 22039.549 Da / Num. of mol.: 16 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: 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: 2.51 Å3/Da / Density % sol: 51.07 % / Description: leaf |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / Details: 1% PEG 4K, 1% MPD, 0.1M NaAC |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.91→50 Å / Num. obs: 93623 / % possible obs: 85.2 % / Redundancy: 2.6 % / Net I/σ(I): 7.676 |
Reflection shell | Resolution: 2.91→2.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.68 / CC1/2: 0.851 / % possible all: 87.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FHA Resolution: 2.91→49.553 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.13 / 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: 2.91→49.553 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.2906 Å / Origin y: 10.1523 Å / Origin z: -7.4546 Å
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Refinement TLS group | Selection details: all |