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Yorodumi- PDB-8a2m: X-ray structure of Ru(bpy)3]2+ complex (Ru1)-encapsulated human h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a2m | ||||||
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Title | X-ray structure of Ru(bpy)3]2+ complex (Ru1)-encapsulated human heavy chain ferritin | ||||||
Components | Ferritin heavy chain, N-terminally processed | ||||||
Keywords | TRANSPORT PROTEIN / human ferritin / heavy chain / antimicrobial peptide / encapsulation / SDS | ||||||
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: 1.57 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: Front Mol Biosci / Year: 2023 Title: A new and efficient procedure to load bioactive molecules within the human heavy-chain ferritin nanocage. Authors: Lucignano, R. / Stanzione, I. / Ferraro, G. / Di Girolamo, R. / Cane, C. / Di Somma, A. / Duilio, A. / Merlino, A. / Picone, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a2m.cif.gz | 66.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a2m.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8a2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/8a2m ftp://data.pdbj.org/pub/pdb/validation_reports/a2/8a2m | HTTPS FTP |
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-Related structure data
Related structure data | 8a2lC 8a5nC 5n27S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21181.512 Da / Num. of mol.: 1 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P02794 | ||||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 59.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 2.0 M magnesium chloride, 0.1 M bicine buffer pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→106.1 Å / Num. obs: 37411 / % possible obs: 99.4 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.25 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.57→1.59 Å / Redundancy: 15 % / Rmerge(I) obs: 1 / Num. unique obs: 1836 / CC1/2: 0.846 / Rpim(I) all: 0.38 / Rrim(I) all: 0.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5n27 Resolution: 1.57→105.622 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.183 / WRfactor Rwork: 0.156 / SU B: 1.235 / SU ML: 0.043 / Average fsc free: 0.9497 / Average fsc work: 0.9544 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.069 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.802 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→105.622 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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