[English] 日本語
Yorodumi- PDB-4iwk: Crystal structure of iron soaked (overnight) ferritin from Pseudo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iwk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of iron soaked (overnight) ferritin from Pseudo-nitzschia multiseries | ||||||
Components | Ferritin | ||||||
Keywords | TRANSPORT PROTEIN / ferritin / 4 helix bundle / iron storage / acetamido-cysteines | ||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudo-nitzschia multiseries (Diatom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Pfaffen, S. / Murphy, M.E.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Mechanism of ferrous iron binding and oxidation by ferritin from a pennate diatom. Authors: Pfaffen, S. / Abdulqadir, R. / Le Brun, N.E. / Murphy, M.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4iwk.cif.gz | 220.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4iwk.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 4iwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iwk_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4iwk_full_validation.pdf.gz | 512.2 KB | Display | |
Data in XML | 4iwk_validation.xml.gz | 49.5 KB | Display | |
Data in CIF | 4iwk_validation.cif.gz | 70.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/4iwk ftp://data.pdbj.org/pub/pdb/validation_reports/iw/4iwk | HTTPS FTP |
-Related structure data
Related structure data | 4ismC 4ispC 4ittC 4itwC 4iwjC 4ixkC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 18866.980 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudo-nitzschia multiseries (Diatom) / Gene: FTN / Production host: Escherichia coli (E. coli) / References: UniProt: B6DMH6 #2: Chemical | ChemComp-FE / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.96 % |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 164004 / % possible obs: 99.6 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.18 / Net I/σ(I): 16.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2132 / WRfactor Rwork: 0.1847 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8666 / SU B: 1.492 / SU ML: 0.051 / SU R Cruickshank DPI: 0.079 / SU Rfree: 0.0811 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 105.05 Å2 / Biso mean: 25.5402 Å2 / Biso min: 7.35 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→47.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
|