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Yorodumi- PDB-6ts1: Crystal structure of human L ferritin (HuLf) triple variant E60A-... -
+Open data
-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 | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / human L ferritin / HuLf / E60A-E61A-E64A / Fe(III) / trinuclear Fe(III) cluster | ||||||
Function / homology | Function and homology information Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / Iron uptake and transport / azurophil granule lumen / iron ion transport ...Scavenging by Class A Receptors / intracellular ferritin complex / autolysosome / Golgi Associated Vesicle Biogenesis / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / Iron uptake and transport / azurophil granule lumen / iron ion transport / intracellular iron ion homeostasis / iron ion binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Pozzi, C. / Ciambellotti, S. / Turano, P. / Mangani, S. | ||||||
Citation | Journal: Chemistry / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ts1.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ts1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ts1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/6ts1 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6ts1 | HTTPS FTP |
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-Related structure data
Related structure data | 6tr9C 6trzC 6ts0C 6tsaC 6tsfC 6tsjC 6tssC 6tsxC 5lg8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Homo sapiens (human) / Gene: FTL / Plasmid: pET-21c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -pLysS / References: UniProt: P02792 |
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-Non-polymers , 5 types, 156 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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