[English] 日本語
![](img/lk-miru.gif)
- PDB-2yqc: Crystal Structure of uridine-diphospho-N-acetylglucosamine pyroph... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2yqc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of uridine-diphospho-N-acetylglucosamine pyrophosphorylase from Candida albicans, in the apo-like form | ||||||
![]() | UDP-N-acetylglucosamine pyrophosphorylase | ||||||
![]() | TRANSFERASE / Pyrophosphorylase / N-acetylglucosamine / Uridine-diphospho-N-acetylglucosamine / N-acetylglucosamine-1-phosphate / Candida albicans | ||||||
Function / homology | ![]() UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miki, K. / Maruyama, D. / Nishitani, Y. / Nonaka, T. / Kita, A. | ||||||
![]() | ![]() Title: Crystal Structure of Uridine-diphospho-N-acetylglucosamine Pyrophosphorylase from Candida albicans and Catalytic Reaction Mechanism Authors: Maruyama, D. / Nishitani, Y. / Nonaka, T. / Kita, A. / Fukami, T.A. / Mio, T. / Yamada-Okabe, H. / Yamada-Okabe, T. / Miki, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 119.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 90.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.3 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2yqhC ![]() 2yqjC ![]() 2yqsC ![]() 1jvdS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54727.832 Da / Num. of mol.: 1 / Mutation: S216L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O74933, UDP-N-acetylglucosamine diphosphorylase |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.06 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 30% PEG 6000, 0.1M ammonium sulfate, 5% glycerol, 0.001M N-acetylglucosamine-1-phosphate, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 28, 2003 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 40383 / % possible obs: 90.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.8 Å2 / Rsym value: 0.111 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 3729 / Rsym value: 0.337 / % possible all: 68.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JVD Resolution: 1.9→39.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1219636.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The intensity of the reflection used for the refinement is more than 0 sigma, but that of the unique reflections in the table of the statistics of the X-ray crystallography at the article is ...Details: The intensity of the reflection used for the refinement is more than 0 sigma, but that of the unique reflections in the table of the statistics of the X-ray crystallography at the article is more than 1 sigma. Therefore, the number of reflections in the refinement section is larger than that in the data collection.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.1034 Å2 / ksol: 0.353506 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→39.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|