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- PDB-3e25: Crystal structure of M. tuberculosis glucosyl-3-phosphoglycerate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3.0E+25 | ||||||
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Title | Crystal structure of M. tuberculosis glucosyl-3-phosphoglycerate synthase | ||||||
![]() | Putative uncharacterized protein | ||||||
![]() | TRANSFERASE / glucosyltransferase / mycobacterial / GT81 UDP-glucose / 3-phosphoglycerate | ||||||
Function / homology | ![]() glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / glycosyltransferase activity / magnesium ion binding / protein homodimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pereira, P.J.B. / Empadinhas, N. / Costa, M.S. / Macedo-Ribeiro, S. | ||||||
![]() | ![]() Title: Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis Authors: Pereira, P.J.B. / Empadinhas, N. / Albuquerque, L. / Sa-Moura, B. / da Costa, M.S. / Macedo-Ribeiro, S. #1: Journal: Fems Microbiol.Lett. / Year: 2008 Title: Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase Authors: Empadinhas, N. / Albuquerque, L. / Mendes, V. / Macedo-Ribeiro, S. / da Costa, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 49.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.2 KB | Display | ![]() |
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Full document | ![]() | 748.6 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35938.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-UDP / |
#4: Chemical | ChemComp-3PG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris pH 8.0, 0.5% polyethyleneglycol monomethyl ether 5000, 0.65M Na-K phosphate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC Q4R / Detector: CCD / Date: Jul 1, 2007 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→70.9 Å / Num. all: 17283 / Num. obs: 16855 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 42.21 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.069 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2481 / Rsym value: 0.33 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Rubrobacter xylanophilus mannosyl-3-phosphoglycerate synthase (Sa-Moura et al., Acta Cryst. (2008). F64, 760-763) Resolution: 2.7→32.335 Å / Occupancy max: 1 / Occupancy min: 0.66 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 25.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.422 Å2 / ksol: 0.324 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.71 Å2 / Biso mean: 45.122 Å2 / Biso min: 23.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→32.335 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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