[English] 日本語
![](img/lk-miru.gif)
- PDB-6fx9: The X-ray structure of the ferritin nanocage containing Au and Pt... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6fx9 | ||||||
---|---|---|---|---|---|---|---|
Title | The X-ray structure of the ferritin nanocage containing Au and Pt, obtained upon encapsulation of a single heterobimetallic compound within the protein cage (synchrtron data) | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL TRANSPORT | ||||||
Function / homology | ![]() : / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Merlino, A. / Ferraro, G. | ||||||
![]() | ![]() Title: Caged noble metals: Encapsulation of a cytotoxic platinum(II)-gold(I) compound within the ferritin nanocage. Authors: Ferraro, G. / Petruk, G. / Maiore, L. / Pane, F. / Amoresano, A. / Cinellu, M.A. / Monti, D.M. / Merlino, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 59.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fx8C ![]() 5erkS S: Starting model for refinement C: citing same article ( |
---|---|
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: 19872.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Non-polymers , 6 types, 248 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/AU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/AU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-AU / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.87 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.6 M ammonium sulfate 0.1 M Tris HCl pH 7.4 60 mM cadmium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→104.9 Å / Num. obs: 41265 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.039 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.9 / CC1/2: 0.592 / Rpim(I) all: 0.279 / % possible all: 99.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5ERK Resolution: 1.5→104.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.134 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.241 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→104.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|