+Open data
-Basic information
Entry | Database: PDB / ID: 5ix6 | ||||||
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Title | X-ray structure of Auoxo3-encapsulated horse spleen apoferritin | ||||||
Components | Ferritin light chain | ||||||
Keywords | TRANSPORT PROTEIN / ferritin / nanocage / metallodrugs / gold compounds | ||||||
Function / homology | Function and homology information : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Ferraro, G. / Pontillo, N. / Merlino, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2016 Title: Gold-based drug encapsulation within a ferritin nanocage: X-ray structure and biological evaluation as a potential anticancer agent of the Auoxo3-loaded protein. Authors: Ferraro, G. / Monti, D.M. / Amoresano, A. / Pontillo, N. / Petruk, G. / Pane, F. / Cinellu, M.A. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ix6.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ix6.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ix6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/5ix6 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/5ix6 | HTTPS FTP |
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-Related structure data
Related structure data | 5erkS S: Starting model for refinement |
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Similar structure data |
-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: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: spleen / References: UniProt: P02791 | ||||||
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#2: Chemical | ChemComp-AU / #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-SO4 / | #5: 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: 3.09 Å3/Da / Density % sol: 60.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Crystals of Auoxo3-encapsulated AFt with diamond-like morphology, suitable for X-ray diffraction data collection, were grown by hanging-drop vapor diffusion technique at 293 K mixing the ...Details: Crystals of Auoxo3-encapsulated AFt with diamond-like morphology, suitable for X-ray diffraction data collection, were grown by hanging-drop vapor diffusion technique at 293 K mixing the protein (5-10 mg x mL-1) with equal volumes of a reservoir solution consisting of 0.6-0.8 M (NH4)2SO4, 0.1 M Tris pH 7.4-7.7, 50-60 mM CdSO4. PH range: 7.4-7.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 17, 2015 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→104.3 Å / Num. obs: 20893 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.666 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.102 / Rrim(I) all: 0.243 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.8 / CC1/2: 0.284 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ERK Resolution: 1.85→104.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.458 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.125 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.717 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→104.3 Å
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Refine LS restraints |
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