[English] 日本語
![](img/lk-miru.gif)
- PDB-2vhe: PglD-CoA complex: An acetyl transferase from Campylobacter jejuni -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vhe | ||||||
---|---|---|---|---|---|---|---|
Title | PglD-CoA complex: An acetyl transferase from Campylobacter jejuni | ||||||
![]() | ACETYLTRANSFERASE | ||||||
![]() | TRANSFERASE / COENZYME A / N-ACETYL TRANSFERASE | ||||||
Function / homology | ![]() UDP-N-acetylbacillosamine N-acetyltransferase / protein N-linked glycosylation via asparagine / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rangarajan, E.S. / Ruane, K.M. / Sulea, T. / Watson, D.C. / Proteau, A. / Leclerc, S. / Cygler, M. / Matte, A. / Young, N.M. | ||||||
![]() | ![]() Title: Structure and Active Site Residues of Pgld, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter Jejuni Authors: Rangarajan, E.S. / Ruane, K.M. / Sulea, T. / Watson, D.C. / Proteau, A. / Leclerc, S. / Cygler, M. / Matte, A. / Young, N.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1022.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bfpC ![]() 2npoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9907, -0.1361, -0.008404), Vector: |
-
Components
#1: Protein | Mass: 21043.553 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q0P9D1, UDP-N-acetylglucosamine diphosphorylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | FIRST XXX CORESPOND TO THE TAG. NO. STARTS FROM ALA 2. EXPAND | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1 M SODIUM CITRATE PH 5.6, 0.16 M SODIUM TARTRATE AND 2.0 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→15 Å / Num. obs: 48692 / % possible obs: 100 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NPO Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.977 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 36-46 AND 182-183 ARE DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.77 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|