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Open data
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Basic information
Entry | Database: PDB / ID: 7w7j | ||||||
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Title | Crystal structure of IrCp* immobilized apo-R52H-rHLFr (25 equiv) | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL TRANSPORT / Iron storage protein / Ir binding / METAL BINDING PROTEIN | ||||||
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 | ![]() ![]() | ||||||
![]() | Taher, M. / Maity, B. / Nakane, T. / Abe, S. / Mazumdar, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Controlled Uptake of an Iridium Complex inside Engineered apo-Ferritin Nanocages: Study of Structure and Catalysis. Authors: Taher, M. / Maity, B. / Nakane, T. / Abe, S. / Ueno, T. / Mazumdar, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.4 KB | Display | ![]() |
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PDB format | ![]() | 42.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7emlC ![]() 7emmC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19853.381 Da / Num. of mol.: 1 / Mutation: R52H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 241 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/IR.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IR.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / | ||||||
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#3: Chemical | ChemComp-IR / | ||||||
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate (0.5-1.0M), Cadmium sulfate(12-20mM) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.086 Å / Num. obs: 41390 / % possible obs: 99.3 % / Redundancy: 4.4 % / CC1/2: 0.997 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 2000 / CC1/2: 0.366 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1dat Resolution: 1.5→19.086 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.167 / WRfactor Rwork: 0.145 / SU B: 1.618 / SU ML: 0.056 / Average fsc free: 0.8938 / Average fsc work: 0.8971 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.067 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: 15.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.086 Å
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Refine LS restraints |
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LS refinement shell |
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