+Open data
-Basic information
Entry | Database: PDB / ID: 6jef | ||||||
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Title | Crystal structure of apo-R168C/L169C-Fr | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / Metal binding | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Abe, S. / Ito, N. / Maity, B. / Lu, C. / Lu, D. / Ueno, T. | ||||||
Citation | Journal: Dalton Trans / Year: 2019 Title: Coordination design of cadmium ions at the 4-fold axis channel of the apo-ferritin cage. Authors: Abe, S. / Ito, N. / Maity, B. / Lu, C. / 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 | 6jef.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jef.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6jef ftp://data.pdbj.org/pub/pdb/validation_reports/je/6jef | HTTPS FTP |
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-Related structure data
Related structure data | 6jeeC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19808.361 Da / Num. of mol.: 1 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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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-CL / | #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: 3.15 Å3/Da / Density % sol: 60.95 % |
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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 210 / Detector: CCD / Date: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→30.01 Å / Num. obs: 35456 / % possible obs: 99.5 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 61.9 |
Reflection shell | Resolution: 1.58→1.61 Å / Rmerge(I) obs: 0.246 / Num. unique obs: 1746 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DAT Resolution: 1.58→27.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.005 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063
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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: 15.799 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→27.71 Å
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Refine LS restraints |
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