+Open data
-Basic information
Entry | Database: PDB / ID: 5lg8 | ||||||
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Title | Human L-type ferritin iron loaded for 60 minutes | ||||||
Components | Ferritin light chain | ||||||
Keywords | METAL BINDING PROTEIN / L-type / ferritin / mineralization / iron | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Pozzi, C. / Di Pisa, F. / Mangani, S. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Chemistry at the protein-mineral interface in L-ferritin assists the assembly of a functional ( mu (3)-oxo)Tris[( mu (2)-peroxo)] triiron(III) cluster. Authors: Pozzi, C. / Ciambellotti, S. / Bernacchioni, C. / Di Pisa, F. / 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 | 5lg8.cif.gz | 58.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lg8.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/5lg8 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/5lg8 | HTTPS FTP |
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-Related structure data
Related structure data | 5lg2C 2fg4S 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 A
#1: Protein | Mass: 20048.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTL / Plasmid: pET21c / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS / References: UniProt: P02792 |
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-Non-polymers , 6 types, 224 molecules
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-OXY / | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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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: 3.65 Å3/Da / Density % sol: 66.28 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Cd(NO3)2, 100 mM ammonium sulfate, and 200 mM sodium acetate pH 5 PH range: 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→29.7 Å / Num. obs: 20846 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Biso Wilson estimate: 15.36 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FG4 Resolution: 1.98→29.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.401 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104
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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: 25.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→29.7 Å
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Refine LS restraints |
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