[English] 日本語
![](img/lk-miru.gif)
- PDB-8j2n: Exopolysaccharide phosphotransferase CpsY in Mycobacterium tuberc... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8j2n | ||||||
---|---|---|---|---|---|---|---|
Title | Exopolysaccharide phosphotransferase CpsY in Mycobacterium tuberculosis | ||||||
![]() | Exopolysaccharide phosphotransferase CpsY | ||||||
![]() | TRANSFERASE / Phosphotransferase CpsY / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) / Gene name Rv0806c / Taxonomic 83332 NCBI / P9WGD1 | ||||||
Function / homology | ![]() transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / polysaccharide biosynthetic process / peptidoglycan-based cell wall Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, D.F. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Exopolysaccharide phosphotransferase CpsY in Mycobacterium tuberculosis Authors: Liu, D.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 116.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 89 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 434 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 36800.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Primary accession P9WGD1 Source: (gene. exp.) ![]() Tissue: Taxonomic identifier 83332 / Gene: cpsY, Rv0806c Organ: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Production host: ![]() ![]() References: UniProt: P9WGD1, Transferases; Transferring phosphorus-containing groups #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.81 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop Details: 0.1 M Citric acid, 0.05 M BIS-TRIS propane, pH 5.8, 15% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→26.1 Å / Num. obs: 81599 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.64→1.67 Å / Rmerge(I) obs: 1.133 / Num. unique obs: 5998 |
-
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→26.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|