[English] 日本語
Yorodumi- PDB-2poc: The crystal structure of isomerase domain of glucosamine-6-phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2poc | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of isomerase domain of glucosamine-6-phosphate synthase from Candida albicans | ||||||
Components | isomerase domain of glutamine-fructose-6-phosphate transaminase (isomerizing) | ||||||
Keywords | TRANSFERASE / glucosamine-6-phosphate synthase / aldose/ketose isomerase / crystal structure / Rossmann-like fold | ||||||
Function / homology | Function and homology information glucosamine biosynthetic process / hyphal growth / chitin biosynthetic process / fungal-type cell wall chitin biosynthetic process / cell wall chitin biosynthetic process / 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 / hyphal growth / chitin biosynthetic process / fungal-type cell wall chitin biosynthetic process / cell wall chitin biosynthetic process / 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 Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Raczynska, J. / Olchowy, J. / Milewski, S. / Rypniewski, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2poc.cif.gz | 303.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2poc.ent.gz | 244 KB | Display | PDB format |
PDBx/mmJSON format | 2poc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/2poc ftp://data.pdbj.org/pub/pdb/validation_reports/po/2poc | HTTPS FTP |
---|
-Related structure data
Related structure data | 2putC 2puvC 2puwC 1moqS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The asymmetric unit contains the tetrameric biological assembly |
-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 40614.738 Da / Num. of mol.: 4 / Fragment: isomerase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / Gene: GFA1 / Plasmid: pET23b-FRU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P53704, glutamine-fructose-6-phosphate transaminase (isomerizing) #2: Sugar | ChemComp-BG6 / |
---|
-Non-polymers , 4 types, 902 molecules
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-UD1 / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M magnesium acetate, 0.1 M sodium cacodylate pH 6.5, 30 % v/v 2-methyl-2,4-pentanediol; 10-fold excess of UDP-GlcNAc and Glc-6-P;, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2006 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8162 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 141467 / Num. obs: 141467 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.07 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.549 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MOQ Resolution: 1.8→19.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.402 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: NULLf
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 27.247 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
|