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Yorodumi- PDB-5jt0: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -
+Open data
-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+ | ||||||
Components | Glucosyl-3-phosphoglycerate synthase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Albesa-Jove, D. / Sancho-Vaello, E. / Rodrigo-Unzueta, A. / Comino, N. / Carreras-Gonzalez, A. / Arrasate, P. / Urresti, S. / Guerin, M.E. | ||||||
Citation | Journal: Structure / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jt0.cif.gz | 71.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jt0.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 5jt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/5jt0 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/5jt0 | HTTPS FTP |
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-Related structure data
Related structure data | 5jqxC 5jsxC 5jucC 5judC 4y6nS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 34683.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: gpgS, Rv1208 / Production host: Escherichia coli (E. coli) References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase |
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#5: Sugar | ChemComp-XDX / ( |
-Non-polymers , 4 types, 31 molecules
#2: Chemical | ChemComp-MN / | ||
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#3: Chemical | ChemComp-UDP / | ||
#4: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97933 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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