+Open data
-Basic information
Entry | Database: PDB / ID: 5lg2 | ||||||
---|---|---|---|---|---|---|---|
Title | Horse 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 intracellular ferritin complex / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5lg2.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5lg2.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/5lg2 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/5lg2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5lg8C 3f32S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24|||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19608.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: FTL / Production host: Equus caballus (horse) / References: UniProt: P02791 |
---|
-Non-polymers , 7 types, 166 molecules
#2: Chemical | #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-OXY / | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.18 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 80 mM Cd(NO3)2, 80 mM ammonium sulfate, and 200 mM sodium acetate pH 5 PH range: 5-6 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.722 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.722 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→23.61 Å / Num. obs: 13146 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.5 % / Biso Wilson estimate: 14.22 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.22→2.34 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F32 Resolution: 2.22→23.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0.178 / SU B: 4.855 / SU ML: 0.121 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.178 Details: Several water molecules involved in the coordination of metal ions were not modeled due to the lack of electron density
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.347 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→23.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|