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- PDB-6tsj: Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tsj | ||||||
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Title | Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 15 minutes | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / human L ferritin / HuLf / 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 | ![]() | 82.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 13.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tr9C ![]() 6trzC ![]() 6ts0C ![]() 6ts1C ![]() 6tsaC ![]() 6tsfC ![]() 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
#1: Protein | Mass: 20048.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-O / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.79 % |
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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 | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07227 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.04 Å / Num. obs: 13632 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.3 % / Biso Wilson estimate: 47.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.02 / Rrim(I) all: 0.091 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 21.7 % / Rmerge(I) obs: 1.041 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1952 / CC1/2: 0.901 / Rpim(I) all: 0.232 / Rrim(I) all: 1.089 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LG8 Resolution: 2.3→43.89 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.211
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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: 47.514 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→43.89 Å
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Refine LS restraints |
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LS refinement shell |
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