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- PDB-6ts1: Crystal structure of human L ferritin (HuLf) triple variant E60A-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ts1 | ||||||
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Title | Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A Fe(III)-loaded for 60 minutes | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / human L ferritin / HuLf / E60A-E61A-E64A / Fe(III) / trinuclear Fe(III) cluster | ||||||
Function / homology | ![]() : / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport ...: / autolysosome / Scavenging by Class A Receptors / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / Iron uptake and transport / ferrous iron binding / azurophil granule lumen / iron ion transport / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozzi, C. / Ciambellotti, S. / Turano, P. / Mangani, S. | ||||||
![]() | ![]() Title: Iron Biomineral Growth from the Initial Nucleation Seed in L-Ferritin. Authors: Ciambellotti, S. / Pozzi, C. / Mangani, S. / Turano, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.8 MB | Display | ![]() |
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Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tr9C ![]() 6trzC ![]() 6ts0C ![]() 6tsaC ![]() 6tsfC ![]() 6tsjC ![]() 6tssC ![]() 6tsxC ![]() 5lg8S 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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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 AAA
#1: Protein | Mass: 19874.572 Da / Num. of mol.: 1 / Mutation: E60A,E61A,E64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 156 molecules ![](data/chem/img/O.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-O / | ||
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#3: Chemical | ChemComp-CD / | ||
#4: Chemical | ChemComp-GOL / | ||
#5: Chemical | ChemComp-FE / #6: 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: 3.69 Å3/Da / Density % sol: 66.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 6TS1 / Observed criterion σ(I): 2 / % possible obs: 100 %
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Reflection shell | % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LG8 Resolution: 2.2→53.522 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.173
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.781 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→53.522 Å
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Refine LS restraints |
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LS refinement shell |
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