+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ygf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of YggS from Fusobacterium nucleatum | ||||||
![]() | Pyridoxal phosphate homeostasis protein | ||||||
![]() | ![]() | ||||||
Function / homology | Uncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | He, S.R. / Chan, Y.Y. / Wang, L.L. / Bai, X. / Bu, T.T. / Zhang, J. / Xu, Y.B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from Fusobacterium nucleatum. Authors: He, S. / Chen, Y. / Wang, L. / Bai, X. / Bu, T. / Zhang, J. / Lu, M. / Ha, N.C. / Quan, C. / Nam, K.H. / Xu, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 125.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26269.314 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: FN0561 / Production host: ![]() ![]() ![]() #2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % |
---|---|
Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.1M sodium acetate trihydrate pH4.8, 0.19M Ammonium Sulfate , 21% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.08→37 Å / Num. obs: 47064 / % possible obs: 97.6 % / Redundancy: 6 % / Biso Wilson estimate: 24.36 Å2 / Rsym value: 0.2 / Net I/σ(I): 27.13 |
Reflection shell | Resolution: 2.08→2.154 Å / Mean I/σ(I) obs: 4.333 / Num. unique obs: 1175 / Rsym value: 0.607 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.61 Å2 / Biso mean: 28.3762 Å2 / Biso min: 10.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.08→37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|