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Open data
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Basic information
Entry | Database: PDB / ID: 3af7 | ||||||
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Title | Crystal Structure of 25Pd(allyl)/apo-Fr | ||||||
![]() | 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 | ![]() | 57 KB | Display | ![]() |
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PDB format | ![]() | 42 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.2 KB | Display | ![]() |
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Full document | ![]() | 471.6 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3af8C ![]() 3af9C ![]() 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: 19872.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 195 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PD.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PD.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / | ||||||
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#3: Chemical | ChemComp-SO4 / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.77 % |
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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: 1.58→30 Å / Num. obs: 35634 / % possible obs: 99.9 % / Redundancy: 12.1 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 1.58→1.64 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.285 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.58→25.17 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.086 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / 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: 15.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→25.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.579→1.62 Å / Total num. of bins used: 20
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