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- PDB-5jud: 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: 5jud | ||||||
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Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with uridine-diphosphate (UDP) - GpgS*UDP | ||||||
![]() | Glucosyl-3-phosphoglycerate synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / metal ion binding 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 | ![]() | 70.8 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 756.2 KB | Display | ![]() |
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Full document | ![]() | 757.8 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jqxC ![]() 5jsxC ![]() 5jt0C ![]() 5jucC ![]() 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
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gpgS, Mb1240 / Production host: ![]() ![]() References: UniProt: Q7U0E1, glucosyl-3-phosphoglycerate synthase |
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#2: Chemical | ChemComp-UDP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.55 Å3/Da / Density % sol: 72.96 % |
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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-F / Detector: PIXEL / Date: Feb 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50.12 Å / Num. obs: 19277 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05358 / Net I/σ(I): 19.98 |
Reflection shell | Resolution: 2.59→2.683 Å / Redundancy: 7 % / Rmerge(I) obs: 0.7833 / Mean I/σ(I) obs: 2.59 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y6N Resolution: 2.59→50.12 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 23.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→50.12 Å
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Refine LS restraints |
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LS refinement shell |
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