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- PDB-9gsr: Crystal Structure of M. hassiacum GPGS co-crystallized with UDP-G... -

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Basic information

Entry
Database: PDB / ID: 9gsr
TitleCrystal Structure of M. hassiacum GPGS co-crystallized with UDP-Glucose (pH 7.2)
ComponentsGlucosyl-3-phosphoglycerate synthase
KeywordsTRANSFERASE / Glucose / UDP / thermostable / GTA-fold
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate synthase / glycosyltransferase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
L(+)-TARTARIC ACID / URIDINE-5'-DIPHOSPHATE / Glucosyl-3-phosphoglycerate synthase
Similarity search - Component
Biological speciesMycolicibacterium hassiacum DSM 44199 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsMacedo-Ribeiro, S. / Nunes-Costa, D. / Silva, A. / Pereira, P.J.B.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT) Portugal
CitationJournal: To Be Published
Title: Crystal Structure of M. Hassiacum GPGS
Authors: Macedo-Ribeiro, S. / Nunes-Costa, D.
History
DepositionSep 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,4116
Polymers70,3022
Non-polymers1,1084
Water9,854547
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-34 kcal/mol
Surface area23330 Å2
Unit cell
Length a, b, c (Å)71.371, 90.548, 95.307
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glucosyl-3-phosphoglycerate synthase


Mass: 35151.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal linker and hexa-histidine tag (KLAAALEHHHHHH)
Source: (gene. exp.) Mycolicibacterium hassiacum DSM 44199 (bacteria)
Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M Potassium Sodium Tartrate pH 7.2, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96112 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96112 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 168628 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 13.07 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.024 / Net I/σ(I): 14.6
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 15671 / Rpim(I) all: 0.352 / % possible all: 83.5

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→48.32 Å / SU ML: 0.1128 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1667 8442 5.01 %
Rwork0.1484 160089 -
obs0.1493 168531 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.93 Å2
Refinement stepCycle: LAST / Resolution: 1.25→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 70 547 4953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714651
X-RAY DIFFRACTIONf_angle_d0.93296388
X-RAY DIFFRACTIONf_chiral_restr0.0753770
X-RAY DIFFRACTIONf_plane_restr0.0156827
X-RAY DIFFRACTIONf_dihedral_angle_d11.86971698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.28252890.26394857X-RAY DIFFRACTION91.48
1.26-1.280.27552680.24255106X-RAY DIFFRACTION94.8
1.28-1.290.24912770.22475164X-RAY DIFFRACTION96.52
1.29-1.310.26182590.21495182X-RAY DIFFRACTION96.78
1.31-1.330.22932600.20665183X-RAY DIFFRACTION97.06
1.33-1.350.22442780.19925214X-RAY DIFFRACTION97.39
1.35-1.370.20972580.19365225X-RAY DIFFRACTION97.51
1.37-1.390.20532880.18925247X-RAY DIFFRACTION97.86
1.39-1.410.21162830.18295281X-RAY DIFFRACTION98.7
1.41-1.430.24322760.18825315X-RAY DIFFRACTION99.34
1.43-1.460.2223030.16925356X-RAY DIFFRACTION99.89
1.46-1.480.19782750.15155373X-RAY DIFFRACTION99.96
1.48-1.510.16772640.14115366X-RAY DIFFRACTION99.79
1.51-1.540.18392830.13135377X-RAY DIFFRACTION99.93
1.54-1.570.15992810.12595350X-RAY DIFFRACTION99.86
1.57-1.610.14672670.12275376X-RAY DIFFRACTION99.93
1.61-1.650.15852620.12065387X-RAY DIFFRACTION99.54
1.65-1.70.14862650.1275400X-RAY DIFFRACTION99.77
1.7-1.750.16073070.12875355X-RAY DIFFRACTION99.93
1.75-1.80.15582910.13215395X-RAY DIFFRACTION99.88
1.8-1.870.14962730.12865379X-RAY DIFFRACTION99.91
1.87-1.940.13833110.12955376X-RAY DIFFRACTION99.98
1.94-2.030.14213030.13075385X-RAY DIFFRACTION99.86
2.03-2.140.14592900.13165395X-RAY DIFFRACTION99.75
2.14-2.270.15452710.13335440X-RAY DIFFRACTION99.91
2.27-2.450.14522730.13015463X-RAY DIFFRACTION99.79
2.45-2.690.14632750.13695449X-RAY DIFFRACTION99.81
2.69-3.080.15932920.15055486X-RAY DIFFRACTION99.67
3.08-3.880.1533280.15095474X-RAY DIFFRACTION99.71
3.88-48.320.18282920.16185733X-RAY DIFFRACTION99.32

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