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- PDB-3e26: Crystal structure of M. tuberculosis glucosyl-3-phosphoglycerate ... -

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Basic information

Entry
Database: PDB / ID: 3.0E+26
TitleCrystal structure of M. tuberculosis glucosyl-3-phosphoglycerate synthase
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / glucosyltransferase / mycobacterial / GT81 UDP-glucose / 3-phosphoglycerate
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPereira, P.J.B. / Empadinhas, N. / Costa, M.S. / Macedo-Ribeiro, S.
Citation
Journal: Plos One / Year: 2008
Title: Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis
Authors: Pereira, P.J.B. / Empadinhas, N. / Albuquerque, L. / Sa-Moura, B. / da Costa, M.S. / Macedo-Ribeiro, S.
#1: Journal: Fems Microbiol.Lett. / Year: 2008
Title: Identification of the mycobacterial glucosyl-3-phosphoglycerate synthase
Authors: Empadinhas, N. / Albuquerque, L. / Mendes, V. / Macedo-Ribeiro, S. / da Costa, M.S.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)35,9381
Polymers35,9381
Non-polymers00
Water2,324129
1
A: Putative uncharacterized protein

A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)71,8762
Polymers71,8762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area2640 Å2
ΔGint-18 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.524, 99.524, 126.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Putative uncharacterized protein / glucosyl-3-phosphoglycerate synthase / GpgS


Mass: 35938.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / Gene: MT1246, Rv1208 / Plasmid: pET30a / Production host: Escherichia coli (E. coli)
References: UniProt: O05309, UniProt: P9WMW9*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 0.5% polyethyleneglycol monomethyl ether 5000, 0.65M Na-K phosphate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 21, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→78.3 Å / Num. all: 21338 / Num. obs: 21338 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 53.97 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.07 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3117 / Rsym value: 0.386 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rubrobacter xylanophilus mannosyl-3-phosphoglycerate synthase (Sa-Moura et al., Acta Cryst. (2008). F64, 760-763)

Resolution: 2.5→70.374 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1060 5.15 %Random
Rwork0.187 19524 --
all0.188 20584 --
obs0.188 20584 96.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.064 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 127.33 Å2 / Biso mean: 65.546 Å2 / Biso min: 42.25 Å2
Baniso -1Baniso -2Baniso -3
1-9.887 Å20 Å2-0 Å2
2--9.887 Å20 Å2
3----19.773 Å2
Refinement stepCycle: LAST / Resolution: 2.5→70.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 0 129 2217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062131
X-RAY DIFFRACTIONf_angle_d0.972910
X-RAY DIFFRACTIONf_chiral_restr0.06347
X-RAY DIFFRACTIONf_plane_restr0.005376
X-RAY DIFFRACTIONf_dihedral_angle_d15.484783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.499-2.6130.2821230.2512255237889
2.613-2.7510.3181220.232323244593
2.751-2.9230.2361220.2122398252095
2.923-3.1490.2591170.2072481259897
3.149-3.4650.2581370.222483262099
3.465-3.9670.261550.1782521267699
3.967-4.9980.1561480.15525122660100
4.998-70.4020.2061360.1762551268799

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