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Open data
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Basic information
Entry | Database: PDB / ID: 3af9 | ||||||
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Title | Crystal Structure of Pd(allyl)/apo-C48AFr | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / Iron Storage Protein / Light Chain Ferritin / Artificial Metalloprotein | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Abe, S. / Hikage, T. / Watanabe, Y. / Kitagawa, S. / Ueno, T. | ||||||
![]() | ![]() Title: Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes into the Protein Nanocage of apo-Ferritin. Authors: Abe, S. / Hikage, T. / Watanabe, Y. / Kitagawa, 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 | ![]() | 55.3 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3af7C ![]() 3af8C ![]() 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 X
#1: Protein | Mass: 19840.363 Da / Num. of mol.: 1 / Mutation: C48A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 166 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/PD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/PD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PLL / | #5: Chemical | ChemComp-PD / | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 26, 2009 |
Radiation | Monochromator: Rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.508 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 22730 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 16.771 Å2 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.272 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.85→25.55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.872 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.087 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→25.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.852→1.899 Å / Total num. of bins used: 20
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