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Open data
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Basic information
Entry | Database: PDB / ID: 2zg8 | ||||||
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Title | Crystal Structure of Pd(allyl)/apo-H49AFr | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / IRON STORAGE PROTEIN / LIGHT CHAIN APOFERRITIN / 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. / Niemeyer, J. / Abe, M. / Ueno, T. / Hikage, T. / Erker, G. / Watanabe, Y. | ||||||
![]() | ![]() Title: Control of the coordination structure of organometallic palladium complexes in an apo-ferritin cage. Authors: Abe, S. / Niemeyer, J. / Abe, M. / Takezawa, Y. / Ueno, T. / Hikage, T. / Erker, G. / 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 | ![]() | 58.3 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.7 KB | Display | ![]() |
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Full document | ![]() | 466.1 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zg7C ![]() 2zg9C ![]() 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: 19789.314 Da / Num. of mol.: 1 / Mutation: H49A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 227 molecules ![](data/chem/img/PD.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PLL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PD / | ||||||
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#3: Chemical | ChemComp-CD / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | IN THE LIGAND PLL, ALL C-C BOND TYPES ARE DELOCALIZESequence details | THE FEATURE OF UNIPROT (FRIL_HORSE, P02791) SHOWS CONFLICT AT THIS POSITION: L -> P (IN REF. 2). | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: ammonium sulfate, cadmium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 20, 2007 |
Radiation | Monochromator: CONFOCAL MIRROS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 34183 / % possible obs: 100 % / Redundancy: 17.8 % / Biso Wilson estimate: 18.007 Å2 / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.284 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.6→25.15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.168 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / 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: 18.223 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→25.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.642 Å / Total num. of bins used: 20
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