[English] 日本語
![](img/lk-miru.gif)
- PDB-2puw: The crystal structure of isomerase domain of glucosamine-6-phosph... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2puw | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from Candida albicans | ||||||
![]() | isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) | ||||||
![]() | TRANSFERASE / glucosamine-6-phosphate synthase / aldose/ketose isomerase / crystal structure / Rossmann-like fold | ||||||
Function / homology | ![]() glucosamine biosynthetic process / chitin biosynthetic process / hyphal growth / : / glutamine-fructose-6-phosphate transaminase (isomerizing) / : / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding ...glucosamine biosynthetic process / chitin biosynthetic process / hyphal growth / : / glutamine-fructose-6-phosphate transaminase (isomerizing) / : / glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / carbohydrate derivative binding / fructose 6-phosphate metabolic process / protein N-linked glycosylation / glutamine metabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Raczynska, J. / Olchowy, J. / Milewski, S. / Rypniewski, W. | ||||||
![]() | ![]() Title: The Crystal and Solution Studies of Glucosamine-6-phosphate Synthase from Candida albicans Authors: Raczynska, J. / Olchowy, J. / Konariev, P.V. / Svergun, D.I. / Milewski, S. / Rypniewski, W. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2005 Title: Crystallization and preliminary X-ray analysis of the isomerase domain of glucosamine-6-phosphate synthase from Candida albicans Authors: Olchowy, J. / Jedrzejczak, R. / Milewski, S. / Rypniewski, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 139.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 109 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1014.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pocSC ![]() 2putC ![]() 2puvC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 40614.738 Da / Num. of mol.: 2 / Fragment: isomerase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P53704, glutamine-fructose-6-phosphate transaminase (isomerizing) #2: Sugar | #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% w/v PEG 600, 0.15M KSCN, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2003 |
Radiation | Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8125 Å / Relative weight: 1 |
Reflection | Resolution: 3.151→20 Å / Num. all: 19526 / Num. obs: 19526 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 70 Å2 / Rsym value: 0.195 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.151→3.2 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 971 / Rsym value: 0.79 / % possible all: 99 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2POC Resolution: 3.151→19.55 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.864 / SU B: 25.518 / SU ML: 0.401 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.465 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.835 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.4003 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.151→19.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.151→3.23 Å / Total num. of bins used: 20
|