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Open data
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Basic information
Entry | Database: PDB / ID: 2z5r | ||||||
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Title | Apo-Fr with high content of Pd ions | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / IRON STORAGE / LIGHT CHAIN APOFERRITIN | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Ueno, T. / Hirata, K. / Abe, M. / Suzuki, M. / Abe, S. / Shimizu, N. / Yamamoto, M. / Takata, M. / Watanabe, Y. | ||||||
![]() | ![]() Title: Process of accumulation of metal ions on the interior surface of apo-ferritin: crystal structures of a series of apo-ferritins containing variable quantities of Pd(II) ions. Authors: Ueno, T. / Abe, M. / Hirata, K. / Abe, S. / Suzuki, M. / Shimizu, N. / Yamamoto, M. / Takata, M. / 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 | ![]() | 51.1 KB | Display | ![]() |
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PDB format | ![]() | 37.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.3 KB | Display | ![]() |
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Full document | ![]() | 432 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z5pC ![]() 2z5qC ![]() 3fi6C ![]() 1datS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#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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#2: Chemical | ChemComp-PD / #3: Chemical | #4: Water | ChemComp-HOH / | |
-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 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 | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→50 Å / Num. obs: 9397 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 39.084 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 33.9 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.69 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 7.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 2.5→45.41 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.833 / SU B: 7.759 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE AUTHORS USED ONLY ONE CRYSTAL FOR TWO DATA COLLECTIONS. DIFFRACTION DATA WERE COLLECTED WITH TWO DIFFERENCE WAVELENGTHS USING ONE CRYSTAL.
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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: 31.593 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.498→2.563 Å / Total num. of bins used: 20
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