+Open data
-Basic information
Entry | Database: PDB / ID: 4lyu | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Fifteen minutes iron loaded frog M ferritin | |||||||||
Components | Ferritin, middle subunit | |||||||||
Keywords | OXIDOREDUCTASE / ferroxidase | |||||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | |||||||||
Biological species | Rana catesbeiana (American bullfrog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Mangani, S. / Di Pisa, F. / Pozzi, C. / Turano, P. / Lalli, D. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Time-lapse anomalous X-ray diffraction shows how Fe(2+) substrate ions move through ferritin protein nanocages to oxidoreductase sites. Authors: Pozzi, C. / Di Pisa, F. / Lalli, D. / Rosa, C. / Theil, E. / Turano, P. / Mangani, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lyu.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lyu.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lyu_validation.pdf.gz | 413.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lyu_full_validation.pdf.gz | 413.3 KB | Display | |
Data in XML | 4lyu_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 4lyu_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4lyu ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4lyu | HTTPS FTP |
-Related structure data
Related structure data | 4lpjC 4lqhC 4lqjC 4lqvC 4lyxC 4mjyC 4mkuC 4ml5C 4mn9C 4my7C 6i36C 3ka3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 24||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20623.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rana catesbeiana (American bullfrog) / Production host: Escherichia coli (E. coli) / References: UniProt: P07798, ferroxidase | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-FE2 / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.81 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.6-2M magnesium chloride, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2398 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 29, 2012 / Details: mirror | |||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.75→41.11 Å / Num. all: 299848 / Num. obs: 27391 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 12.875 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.3 | |||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3KA3 Resolution: 1.75→31.08 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.47 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.095 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.92 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→31.08 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
|