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Yorodumi- PDB-4ddz: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ddz | ||||||
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Title | Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis | ||||||
Components | GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GpgS) | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information glucosyl-3-phosphoglycerate synthase / UDP-glucose metabolic process / hexosyltransferase activity / glycosyltransferase activity / magnesium ion binding / protein homodimerization activity / metal ion binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Albesa-Jove, D. / Urresti, S. / Gest, P.M. / van der Woerd, M. / Jackson, M. / Guerin, M.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Mechanistic insights into the retaining glucosyl-3-phosphoglycerate synthase from mycobacteria. Authors: Urresti, S. / Albesa-Jove, D. / Schaeffer, F. / Pham, H.T. / Kaur, D. / Gest, P. / van der Woerd, M.J. / Carreras-Gonzalez, A. / Lopez-Fernandez, S. / Alzari, P.M. / Brennan, P.J. / Jackson, M. / 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 | 4ddz.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ddz.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ddz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/4ddz ftp://data.pdbj.org/pub/pdb/validation_reports/dd/4ddz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36582.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gpgS, MT1246, Rv1208 / Plasmid: pET28a-gpgS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases | ||
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#2: Chemical | #3: 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: 4.26 Å3/Da / Density % sol: 71.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1 mM MgCl2, 100 mM sodium cacodylate pH 6.5, 200 mM trisodium citrate, 30%(v/v) 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jul 22, 2008 |
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→41.77 Å / Num. obs: 37009 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 49.73 Å2 / Rsym value: 0.106 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / Num. unique all: 1855 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→34.949 Å / SU ML: 0.82 / σ(F): 1.16 / Phase error: 26.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.48 Å2 / ksol: 0.378 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→34.949 Å
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Refine LS restraints |
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LS refinement shell |
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