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Yorodumi- PDB-7bon: Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bon | ||||||
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Title | Crystal structure of recombinant horse spleen apo-R52C/E56C/R59C/E63C-Fr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / IRON STORAGE | ||||||
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: 1.48 Å | ||||||
Authors | Hishikawa, Y. / Maity, B. / Ito, N. / Abe, S. / Lu, D. / Ueno, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Chem Lett. / Year: 2021 Title: Design of Multinuclear Gold Binding Site at the Two-fold Symmetric Interface of the Ferritin Cage Authors: Hishikawa, Y. / Maity, B. / Ito, N. / Abe, S. / Lu, D. / Ueno, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bon.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bon.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bon_validation.pdf.gz | 9.2 MB | Display | wwPDB validaton report |
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Full document | 7bon_full_validation.pdf.gz | 9.2 MB | Display | |
Data in XML | 7bon_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 7bon_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/7bon ftp://data.pdbj.org/pub/pdb/validation_reports/bo/7bon | HTTPS FTP |
-Related structure data
Related structure data | 7bomC 1datS 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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1 |
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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: 19712.383 Da / Num. of mol.: 1 / Mutation: R53C,E57C,R60C,E64C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Escherichia coli (E. coli) / References: UniProt: P02791 |
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-Non-polymers , 5 types, 220 molecules
#2: Chemical | ChemComp-SO4 / | ||||||
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#3: Chemical | ChemComp-CD / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-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: 3.26 Å3/Da / Density % sol: 62.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→25.45 Å / Num. obs: 43077 / % possible obs: 99.54 % / Redundancy: 5.5 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.08 / Net I/σ(I): 12.76 |
Reflection shell | Resolution: 1.48→1.533 Å / Num. unique obs: 4221 / CC1/2: 0.954 / CC star: 0.988 / Rpim(I) all: 0.131 / Rrim(I) all: 0.309 / % possible all: 99.91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.48→25.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.811 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.057
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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: 15.338 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→25.45 Å
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Refine LS restraints |
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