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- PDB-5jqx: 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: 5jqx | ||||||
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Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with phosphoglyceric acid (PGA) - GpgS*PGA | ||||||
![]() | 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 | ![]() | 216.8 KB | Display | ![]() |
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PDB format | ![]() | 172.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.9 KB | Display | ![]() |
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Full document | ![]() | 476.6 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jsxC ![]() 5jt0C ![]() 5jucC ![]() 5judC ![]() 4decS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gpgS, Rv1208 / Production host: ![]() ![]() References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase #2: Chemical | ChemComp-3PG / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.26 % |
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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 PILATUS 6M / Detector: PIXEL / Date: May 5, 2014 |
Radiation | Monochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→44.504 Å / Num. obs: 58106 / % possible obs: 99.37 % / Redundancy: 3 % / Biso Wilson estimate: 67.53 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06619 / Net I/σ(I): 10.48 |
Reflection shell | Resolution: 2.82→2.921 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5487 / Mean I/σ(I) obs: 2.29 / % possible all: 99.09 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DEC Resolution: 2.82→44.504 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 27.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→44.504 Å
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Refine LS restraints |
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LS refinement shell |
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