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Open data
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Basic information
Entry | Database: PDB / ID: 5e2d | ||||||
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Title | Crystal structure of IrCp*/Pd(allyl)-apo-Fr | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / IRON STORAGE | ||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maity, B. / Fukumori, K. / Abe, S. / Ueno, T. | ||||||
![]() | ![]() Title: Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartments Authors: Maity, B. / Fukumori, K. / Abe, S. / Ueno, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
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PDB format | ![]() | 40.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.3 KB | Display | ![]() |
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Full document | ![]() | 458.3 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e1uC ![]() 5hqoC ![]() 1datS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 19872.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 123 molecules ![](data/chem/img/IR3.gif)
![](data/chem/img/IR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/PD.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/PD.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-IR3 / #3: Chemical | ChemComp-IR / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PD / | #7: Chemical | ChemComp-CD / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulphate, Cadmium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.10461 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→40 Å / Num. obs: 21653 / % possible obs: 100 % / Redundancy: 11 % / Net I/σ(I): 60.3 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 11.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.87→32.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.833 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.858 Å2
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Refinement step | Cycle: 1 / Resolution: 1.87→32.03 Å
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Refine LS restraints |
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