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- PDB-8i77: Crystal structure of horse spleen L-ferritin A115V mutant at -180... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i77 | ||||||
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Title | Crystal structure of horse spleen L-ferritin A115V mutant at -180deg Celsius. | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / Ferritin / A115V mutant / X-ray structure | ||||||
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 | ![]() | 62.2 KB | Display | ![]() |
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PDB format | ![]() | 43 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.6 KB | Display | ![]() |
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Full document | ![]() | 441.8 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i6lC ![]() 8i81C ![]() 8i8qC ![]() 8i8uC ![]() 1datS S: Starting model for refinement 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 A
#1: Protein | Mass: 19900.482 Da / Num. of mol.: 1 / Mutation: A115V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 275 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / | #5: Chemical | #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: 3.14 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) Temp details: non-shaking incubation |
-Data collection
Diffraction | Mean temperature: 293.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Aug 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541838 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30.721 Å / Num. obs: 41611 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.088 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.742 / Num. unique obs: 2029 / CC1/2: 0.806 / Rrim(I) all: 0.836 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DAT Resolution: 1.5→30.721 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.997 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.057 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: 12.033 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.721 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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