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Open data
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Basic information
Entry | Database: PDB / ID: 8j0x | ||||||
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Title | Crystal structure of horse spleen L-ferritin at -20deg Celsius. | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / Ferritin / -20deg Celsius | ||||||
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 | ![]() ![]() | ||||||
![]() | Maity, B. / Tian, J. / Abe, S. / Ueno, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic-Level Insights into a Unique Semi-Clathrate Hydrate Formed in a Confined Environment of Porous Protein Crystal. Authors: Maity, B. / Tian, J. / Furuta, T. / Abe, S. / Ueno, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59 KB | Display | ![]() |
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PDB format | ![]() | 40.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.3 KB | Display | ![]() |
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Full document | ![]() | 447.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j0uC ![]() 8j0vC ![]() 8j0wC ![]() 8j0yC ![]() 8j0zC ![]() 8j10C ![]() 8j11C ![]() 8j16C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 19872.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 169 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) Temp details: Non-shaking incubation. |
-Data collection
Diffraction | Mean temperature: 253.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 8, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22.286 Å / Num. obs: 34348 / % possible obs: 98.9 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1665 / CC1/2: 0.708 / Rpim(I) all: 0.404 / Rrim(I) all: 0.732 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.359 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→22.286 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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