+Open data
-Basic information
Entry | Database: PDB / ID: 6ke4 | ||||||
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Title | ABloop reengineered Ferritin Nanocage | ||||||
Components | Ferritin heavy chain | ||||||
Keywords | METAL BINDING PROTEIN / rHuHF / ABloop reengineered | ||||||
Function / homology | Function and homology information iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / negative regulation of fibroblast proliferation / ferric iron binding ...iron ion sequestering activity / Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / 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: 2.3 Å | ||||||
Authors | Wang, W.M. / Wang, H.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2019 Title: AB loop engineered ferritin nanocages for drug loading under benign experimental conditions. Authors: Wang, W. / Wang, L. / Li, G. / Zhao, G. / Zhao, X. / Wang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ke4.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ke4.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ke4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/6ke4 ftp://data.pdbj.org/pub/pdb/validation_reports/ke/6ke4 | HTTPS FTP |
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-Related structure data
Related structure data | 6ke2C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20867.232 Da / Num. of mol.: 1 / Mutation: Deletion,K84Q 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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-Non-polymers , 5 types, 137 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.22 Å3/Da / Density % sol: 61.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bincine pH 9.0, 2M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.99779 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99779 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 12159 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.62 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 533 / Rrim(I) all: 0.424 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FHA Resolution: 2.3→30.44 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.37 Å2 / Biso mean: 20.3401 Å2 / Biso min: 4.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→30.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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