+Open data
-Basic information
Entry | Database: PDB / ID: 8b7l | ||||||
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Title | X-ray structure of Auranofin-horse spleen ferritin | ||||||
Components | Ferritin light chain | ||||||
Keywords | TRANSPORT PROTEIN / ferritin / gold / encapsulation / auranofin / anticancer | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Ferraro, G. / Merlino, A. | ||||||
Funding support | 1items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Evaluation of Auranofin Loading within Ferritin Nanocages. Authors: Lucignano, R. / Pratesi, A. / Imbimbo, P. / Monti, D.M. / Picone, D. / Messori, L. / Ferraro, G. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b7l.cif.gz | 66.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b7l.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8b7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/8b7l ftp://data.pdbj.org/pub/pdb/validation_reports/b7/8b7l | HTTPS FTP |
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-Related structure data
Related structure data | 8b7oC 5erkS 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
-Protein , 1 types, 1 molecules AAA
#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, 351 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-AU / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 61.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.8 M ammonium sulphate 0.1 M TrisHCl pH 7.4 60 mM cadmium sulphate |
-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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→64.34 Å / Num. obs: 88885 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.014 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.24→1.26 Å / Redundancy: 15 % / Rmerge(I) obs: 1.8 / Num. unique obs: 3593 / CC1/2: 0.772 / Rpim(I) all: 0.364 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ERK Resolution: 1.24→64.34 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.5 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.032 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: 15.916 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→64.34 Å
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Refine LS restraints |
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LS refinement shell |
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