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- PDB-2puv: The crystal structure of isomerase domain of glucosamine-6-phosph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2puv | ||||||
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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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 300.5 KB | Display | ![]() |
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PDB format | ![]() | 241.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 59 KB | Display | |
Data in CIF | ![]() | 83.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2pocSC ![]() 2putC ![]() 2puwC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The asymmetric unit contains the tetrameric biological assembly |
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Components
-Protein , 1 types, 4 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.) ![]() ![]() ![]() References: UniProt: P53704, glutamine-fructose-6-phosphate transaminase (isomerizing) |
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-Non-polymers , 5 types, 783 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/M6R.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/UD1.gif)
![](data/chem/img/M6R.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-UD1 / #5: Chemical | ChemComp-M6R / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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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; crystals soaked with large excess of 2-amino-2-deoxy-D- ...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; crystals soaked with large excess of 2-amino-2-deoxy-D-mannitol 6-phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 8, 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: 1.9→20 Å / Num. all: 120934 / Num. obs: 120934 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.058 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 5743 / Rsym value: 0.474 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2POC Resolution: 1.9→19.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.803 / SU ML: 0.085 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 25.539 Å2
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Refine analyze | Luzzati sigma a obs: 0.0845 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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