[English] 日本語
![](img/lk-miru.gif)
- PDB-3qz3: The crystal structure of ferritin from Vibrio cholerae O1 biovar ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3qz3 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of ferritin from Vibrio cholerae O1 biovar El Tor str. N16961 | ||||||
![]() | Ferritin | ||||||
![]() | OXIDOREDUCTASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / all alpha ferritin-like / cytoplasmic | ||||||
Function / homology | ![]() bacterial non-heme ferritin / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / ferrous iron binding / iron ion transport / iron ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: The crystal structure of ferritin from Vibrio cholerae O1 biovar El Tor str. N16961 Authors: Tan, K. / Mulligan, R. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 209.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 169.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 462.8 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1eumS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 8||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21288.809 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: N16961 / Gene: VC_0078 / Plasmid: pMCSG19C / Production host: ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.31 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M NaCl, 0.1M Bis-tris, 1.5M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41 Å / Num. all: 42655 / Num. obs: 42655 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2095 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EUM Resolution: 2.099→41.028 Å / SU ML: 0.23 / σ(F): 0 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.994 Å2 / ksol: 0.352 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.099→41.028 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|