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Yorodumi- PDB-6fx8: The X-ray structure of the ferritin nanocage containing Au and Pt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fx8 | ||||||
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Title | The X-ray structure of the ferritin nanocage containing Au and Pt, obtained upon encapsulation of a single heterobimetallic compound within the protein cage (rotating anode data) | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL TRANSPORT | ||||||
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: 1.8 Å | ||||||
Authors | Merlino, A. / Ferraro, G. | ||||||
Citation | Journal: Int. J. Biol. Macromol. / Year: 2018 Title: Caged noble metals: Encapsulation of a cytotoxic platinum(II)-gold(I) compound within the ferritin nanocage. Authors: Ferraro, G. / Petruk, G. / Maiore, L. / Pane, F. / Amoresano, A. / Cinellu, M.A. / Monti, D.M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fx8.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fx8.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 6fx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fx8_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 6fx8_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 6fx8_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 6fx8_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/6fx8 ftp://data.pdbj.org/pub/pdb/validation_reports/fx/6fx8 | HTTPS FTP |
-Related structure data
Related structure data | 6fx9C 5erkS 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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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: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02791 |
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-Non-polymers , 5 types, 277 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-AU / | #6: 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: 3.1 Å3/Da / Density % sol: 60.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.6 M ammonium sulfate 0.1 M Tris HCl pH 7.4 60 mM cadmium sulfate |
-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: Jun 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→104.4 Å / Num. obs: 24060 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.052 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.402 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ERK Resolution: 1.8→104.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.215 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / 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: 17.878 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→104.4 Å
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Refine LS restraints |
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