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- PDB-5jqq: Crystal structure of glucosyl-3-phosphoglycerate synthase from My... -

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Database: PDB / ID: 5jqq
TitleCrystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form
ComponentsGlucosyl-3-phosphoglycerate synthase
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
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
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Ra (unknown)
AuthorsAlbesa-Jove, D. / Urresti, S. / Gest, P.M. / van der Woerd, M. / Jackson, M. / Guerin, M.E.
CitationJournal: To Be Published
Title: Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis - apo form
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.
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release

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Deposited unit
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

Theoretical massNumber of molelcules
Total (without water)36,7673
A: Glucosyl-3-phosphoglycerate synthase
hetero molecules

A: Glucosyl-3-phosphoglycerate synthase
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 area4010 Å2
ΔGint-25 kcal/mol
Surface area20640 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



#1: Protein Glucosyl-3-phosphoglycerate synthase /

Mass: 36582.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Ra (unknown)
Gene: gpgS, Rv1208 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WMW9, glucosyl-3-phosphoglycerate synthase
#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.: 59 / 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
Details: Rosenbaum-Rock Si(111) sagitally focused monochromator
RadiationProtocol: 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 % / Redundancy: 7 % / Rsym value: 0.106 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 100


Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CKJ
Resolution: 2.6→39.077 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 26.54
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 1904 5.14 %Random selection
Rwork0.2089 ---
obs0.2101 37009 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 12 59 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072224
X-RAY DIFFRACTIONf_angle_d1.1533037
X-RAY DIFFRACTIONf_dihedral_angle_d13.115810
X-RAY DIFFRACTIONf_chiral_restr0.047364
X-RAY DIFFRACTIONf_plane_restr0.007390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.66520.35111290.33712408X-RAY DIFFRACTION100
2.6652-2.73730.38581580.33122522X-RAY DIFFRACTION100
2.7373-2.81780.34261040.26872513X-RAY DIFFRACTION100
2.8178-2.90870.24491350.25422582X-RAY DIFFRACTION100
2.9087-3.01260.25131200.24722513X-RAY DIFFRACTION100
3.0126-3.13320.28081510.23842512X-RAY DIFFRACTION100
3.1332-3.27570.2581120.24122485X-RAY DIFFRACTION100
3.2757-3.44830.34681500.24122511X-RAY DIFFRACTION100
3.4483-3.66420.23891510.19532517X-RAY DIFFRACTION100
3.6642-3.94690.21631670.2022502X-RAY DIFFRACTION100
3.9469-4.34360.19941400.17962492X-RAY DIFFRACTION100
4.3436-4.97110.18011400.15772518X-RAY DIFFRACTION100
4.9711-6.25890.22371380.19822505X-RAY DIFFRACTION100
6.2589-39.08120.1761090.1852525X-RAY DIFFRACTION100

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