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- PDB-5jsx: 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: 5jsx | ||||||
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Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis in complex with Mn2+ and uridine-diphosphate-glucose (UDP-Glc) | ||||||
![]() | glucosyl-3-phosphoglycerate synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
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 | ![]() | 72.8 KB | Display | ![]() |
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PDB format | ![]() | 51.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.4 KB | Display | ![]() |
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Full document | ![]() | 805.3 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jqxC ![]() 5jt0C ![]() 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
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MRA_1217 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-UPG / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.66 % |
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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 | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→69.85 Å / Num. obs: 14927 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 85.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06335 / Net I/σ(I): 14.52 |
Reflection shell | Resolution: 2.81→2.91 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.4811 / Mean I/σ(I) obs: 2.6 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Y6N Resolution: 2.81→41.76 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 25.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→41.76 Å
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Refine LS restraints |
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LS refinement shell |
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