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Open data
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Basic information
Entry | Database: PDB / ID: 3fi6 | ||||||
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Title | apo-H49AFr with high content of Pd ions | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / Iron storage / light chain apoferritin | ||||||
Function / homology | ![]() ferritin complex / autolysosome / : / ferric iron binding / autophagosome / ferrous iron binding / iron ion transport / cytoplasmic vesicle / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Abe, M. / Ueno, T. / Hirata, K. / Suzuki, M. / Abe, S. / Shimizu, N. / Yamaoto, 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 | ![]() | 54.9 KB | Display | ![]() |
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PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.8 KB | Display | ![]() |
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Full document | ![]() | 443.1 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z5pC ![]() 2z5qC ![]() 2z5rC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19789.314 Da / Num. of mol.: 1 / Mutation: H49A, L93P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-PD / #3: Chemical | ChemComp-CD / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Sequence details | THE FEATURE OF UNIPROT (FRIL_HORSE, P02791) SHOWS CONFLICT AT THIS POSITION: L -> P (IN REF. 2).' | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.4 % |
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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 | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 23, 2008 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 24004 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 57.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DAT Resolution: 1.8→21.3 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.755 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / 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: 20.797 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→21.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Total num. of bins used: 20
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