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Open data
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Basic information
Entry | Database: PDB / ID: 2z5p | ||||||
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Title | Apo-Fr with low content of Pd ions | ||||||
![]() | Ferritin light chain![]() | ||||||
![]() | METAL BINDING PROTEIN / IRON STORAGE / LIGHT CHAIN APOFERRITIN | ||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ![]() ![]() ![]() 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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Remark 999 | SEQUENCE THE FEATURE OF UNIPROT (FRIL_HORSE, P02791) SHOWS CONFLICT AT THIS POSITION: L -> P (in Ref. 2). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.7 KB | Display | ![]() |
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PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2z5qC ![]() 2z5rC ![]() 3fi6C ![]() 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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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, 252 molecules ![](data/chem/img/PD.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-PD / ![]() #3: Chemical | #4: Chemical | ![]() #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % |
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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: 1.65→50 Å / Num. obs: 30995 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.5 % / Biso Wilson estimate: 15.581 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 40 | |||||||||||||||
Reflection shell | Resolution: 1.65→1.693 Å / Redundancy: 22.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 14.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1DAT Resolution: 1.65→34.79 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.215 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / 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: 17.148 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→34.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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