[English] 日本語
![](img/lk-miru.gif)
- PDB-7rzx: Crystal Structure of Ferritin grown by microbatch method in prese... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7rzx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Ferritin grown by microbatch method in presence of agarose and electric field 4.3KV | ||||||
![]() | Ferritin light chain | ||||||
![]() | METAL BINDING PROTEIN / ferritin / crystallization / agarose / electric field / metal ions | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, J.D. / Stojanoff, V. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal Structure of Ferritin grown by microbatch method in presence of agarose and electric field 4.3KV Authors: Aditya, S. / Priyadharshine, R. / Maham, I. / Miller, J.D. / Stojanoff, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 51.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 440.2 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w0oS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 24|||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 19872.428 Da / Num. of mol.: 1 / Fragment: residue 3-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.48 % |
---|---|
Crystal grow | Temperature: 290 K / Method: microbatch / Details: CdSO4,NH4SO4,Tris pH7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC HF-4M / Detector: PIXEL / Date: Aug 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→28.63 Å / Num. obs: 9949 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 35.88 Å2 / CC1/2: 0.998 / Net I/σ(I): 0.828 |
Reflection shell | Resolution: 2.44→2.51 Å / Num. unique obs: 704 / CC1/2: 0.766 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2W0O Resolution: 2.44→28.63 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.83 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 227.7 Å2 / Biso mean: 38.6369 Å2 / Biso min: 22.04 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.44→28.63 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
|