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Yorodumi- PDB-5mik: X-ray structure of carboplatin-encapsulated horse spleen apoferri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mik | ||||||
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Title | X-ray structure of carboplatin-encapsulated horse spleen apoferritin (rotating anode data) | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL TRANSPORT | ||||||
Function / homology | Function and homology information intracellular ferritin complex / 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: 1.96 Å | ||||||
Authors | Pontillo, N. / Ferraro, G. / Helliwell, J.R. / Merlino, A. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: X-ray Structure of the Carboplatin-Loaded Apo-Ferritin Nanocage. Authors: Pontillo, N. / Ferraro, G. / Helliwell, J.R. / Amoresano, 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 | 5mik.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mik.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/5mik ftp://data.pdbj.org/pub/pdb/validation_reports/mi/5mik | HTTPS FTP |
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-Related structure data
Related structure data | 5mijC 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 , 6 types, 209 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | #6: Chemical | #7: 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: 3.09 Å3/Da / Density % sol: 60.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 0.8 M (NH4)2SO4, 0.1 M Tris pH 7.7, 60 mM CdSO4. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 10, 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: 1.96→104.3 Å / Num. obs: 18700 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.96→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5erk Resolution: 1.96→104.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.795 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.119 / 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: 20.803 Å2
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Refinement step | Cycle: 1 / Resolution: 1.96→104.3 Å
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Refine LS restraints |
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