[English] 日本語
![](img/lk-miru.gif)
- PDB-5j8s: Iron-free state of Rana Catesbeiana H' ferritin variant E57A/E136... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5j8s | ||||||
---|---|---|---|---|---|---|---|
Title | Iron-free state of Rana Catesbeiana H' ferritin variant E57A/E136A/D140A | ||||||
![]() | Ferritin, middle subunit | ||||||
![]() | OXIDOREDUCTASE / Rana Catesbeiana / ferritin variant / ferroxidase activity / M type / H' type / oxidoreductase activity / iron | ||||||
Function / homology | ![]() ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm Similarity search - Function | ||||||
Biological species | Lithobates catesbeiana (American bullfrog) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pozzi, C. / Di Pisa, F. / Mangani, S. / Bernacchioni, C. / Turano, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Ferroxidase Activity in Eukaryotic Ferritin is Controlled by Accessory-Iron-Binding Sites in the Catalytic Cavity. Authors: Bernacchioni, C. / Pozzi, C. / Di Pisa, F. / Mangani, S. / Turano, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 65.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 419.6 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5j8wC ![]() 5j93C ![]() 5j9vC ![]() 5jacC ![]() 4lqhS 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
#1: Protein | Mass: 20463.100 Da / Num. of mol.: 1 / Mutation: E57A, E136A, D140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lithobates catesbeiana (American bullfrog) Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % / Description: Octahedral Crystals |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / Details: 1.6-2.0 M MgCl2 and 0.1 M bicine pH 9.0 / PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2013 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0039 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.25 Å / Num. obs: 43845 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4LQH Resolution: 1.5→37.77 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / Rfactor Rfree error: 0.059 / SU B: 0.931 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.059
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.033 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→37.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|