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- PDB-5jt0: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jt0 | ||||||
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Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+, uridine-diphosphate (UDP) and glucosyl-3-phosphoglycerate (GPG) - GpgS*GPG*UDP*Mn2+ | ||||||
![]() | Glucosyl-3-phosphoglycerate synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Albesa-Jove, D. / Sancho-Vaello, E. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Guerin, M.E. | ||||||
![]() | ![]() Title: Structural Snapshots and Loop Dynamics along the Catalytic Cycle of Glycosyltransferase GpgS. Authors: Albesa-Jove, D. / Romero-Garcia, J. / Sancho-Vaello, E. / Contreras, F.X. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Biarnes, X. / Planas, A. / Guerin, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.3 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5jqxC ![]() 5jsxC ![]() 5jucC ![]() 5judC ![]() 4y6nS C: citing same article ( S: Starting model for refinement |
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Similar 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
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/XDX.gif)
![](data/chem/img/XDX.gif)
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase |
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#5: Sugar | ChemComp-XDX / ( |
-Non-polymers , 4 types, 31 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UDP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / | ||
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#3: Chemical | ChemComp-UDP / | ||
#4: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.48 Å3/Da / Density % sol: 72.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14% PEG 8,000, 0.3-0.5 M Li sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 27, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→69.82 Å / Num. obs: 21639 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 62.91 Å2 / Rmerge(I) obs: 0.0957 / Net I/σ(I): 7.93 |
Reflection shell | Resolution: 2.48→2.569 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.96 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y6N Resolution: 2.8→69.816 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.83 / 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 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→69.816 Å
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Refine LS restraints |
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LS refinement shell |
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