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Open data
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Basic information
Entry | Database: PDB / ID: 3h7g | ||||||
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Title | Apo-FR with AU ions | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / IRON STORAGE / LIGHT CHAIN APOFERRITIN / Iron | ||||||
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, M. / Ueno, T. / Abe, S. / Suzuki, M. / Goto, T. / Toda, Y. / Akita, T. / Yamada, Y. / Watanabe, Y. | ||||||
![]() | ![]() Title: Preparation and catalytic reaction of Au/Pd bimetallic nanoparticles in apo-ferritin Authors: Suzuki, M. / Abe, M. / Ueno, T. / Abe, S. / Goto, T. / Toda, Y. / Akita, T. / Yamada, Y. / Watanabe, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.3 KB | Display | ![]() |
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PDB format | ![]() | 41.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.9 KB | Display | ![]() |
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Full document | ![]() | 446.4 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1datS 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: 19856.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 193 molecules ![](data/chem/img/AU3.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AU3 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | REFER TO THE DATABASE, P02791, REF. 2 FOR THIS CONFLICT. THIS SEQUENCE IS FROM BAA03396 IN GENBANK DATABASE. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: AMMONIUM SULFATE, CADMIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.65→35 Å / Num. obs: 31508 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.2 % / Biso Wilson estimate: 16.79 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 67.8 | ||||||||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 14 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.01 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.65→30.28 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.912 / SU B: 1.25 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.093 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→30.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.69 Å / Total num. of bins used: 20
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