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Yorodumi- PDB-6tr9: Crystal structure of human L ferritin (HuLf) triple variant E60A-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tr9 | ||||||
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Title | Crystal structure of human L ferritin (HuLf) triple variant E60A-E61A-E64A | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / human L ferritin / HuLf / E60A-E61A-E64A | ||||||
Function / homology | Function and homology information : / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 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 | 6tr9.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tr9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tr9_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 6tr9_full_validation.pdf.gz | 424.6 KB | Display | |
Data in XML | 6tr9_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 6tr9_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/6tr9 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/6tr9 | HTTPS FTP |
-Related structure data
Related structure data | 6trzC 6ts0C 6ts1C 6tsaC 6tsfC 6tsjC 6tssC 6tsxC 5lg8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 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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#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 66.63 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→75.61 Å / Num. obs: 11055 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21.2 % / Biso Wilson estimate: 50.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.024 / Rrim(I) all: 0.112 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.46→2.59 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1562 / CC1/2: 0.929 / Rpim(I) all: 0.233 / Rrim(I) all: 1.09 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LG8 Resolution: 2.46→61.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.246
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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: 47.624 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→61.81 Å
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Refine LS restraints |
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LS refinement shell |
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