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- PDB-4ddz: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

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Database: PDB / ID: 4ddz
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis
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
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
Glucosyl-3-phosphoglycerate synthase / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (unknown)
AuthorsAlbesa-Jove, D. / Urresti, S. / Gest, P.M. / van der Woerd, M. / Jackson, M. / Guerin, M.E.
CitationJournal: 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.
DepositionJan 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Jan 9, 2013Group: Database references

Structure visualization

Structure viewerMolecule:

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Deposited unit
hetero molecules

Theoretical massNumber of molelcules
Total (without water)36,7673
hetero molecules

hetero molecules

Theoretical massNumber of molelcules
Total (without water)73,5346
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4030 Å2
ΔGint-28 kcal/mol
Surface area20710 Å2
Unit cell
Length a, b, c (Å)98.850, 98.850, 127.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions




Mass: 36582.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol

Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.14 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 22, 2008
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / Num. unique all: 1855


Blu-Icedata collection
PHENIX(phenix.refine: 1.7.2_869)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 1902 5.14 %RANDOM
Rwork0.2147 ---
obs0.2163 37009 99.79 %-
Solvent computationShrinkage 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
Baniso -1Baniso -2Baniso -3
1-10.2223 Å20 Å2-0 Å2
2--10.2223 Å20 Å2
3----20.4445 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 12 61 2128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162196
X-RAY DIFFRACTIONf_angle_d1.4293005
X-RAY DIFFRACTIONf_dihedral_angle_d13.962798
X-RAY DIFFRACTIONf_chiral_restr0.088361
X-RAY DIFFRACTIONf_plane_restr0.014386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.66520.34961290.3382408X-RAY DIFFRACTION100
2.6652-2.73720.40051580.33732522X-RAY DIFFRACTION100
2.7372-2.81770.31881040.27082513X-RAY DIFFRACTION100
2.8177-2.90870.24961350.24912584X-RAY DIFFRACTION100
2.9087-3.01260.25371200.24532514X-RAY DIFFRACTION100
3.0126-3.13310.29061510.23572512X-RAY DIFFRACTION100
3.1331-3.27560.27151120.23452486X-RAY DIFFRACTION100
3.2756-3.44810.28971500.22332511X-RAY DIFFRACTION100
3.4481-3.6640.25271510.20962514X-RAY DIFFRACTION100
3.664-3.94650.22221670.20822505X-RAY DIFFRACTION100
3.9465-4.3430.23111400.1922488X-RAY DIFFRACTION100
4.343-4.96990.19331400.16722510X-RAY DIFFRACTION100
4.9699-6.25570.26631380.20282517X-RAY DIFFRACTION100
6.2557-34.95190.19971070.20032523X-RAY DIFFRACTION100

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