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- PDB-8hjn: Crystal structure of glycosyltransferase SgUGT94-289-3 in complex... -

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Basic information

Entry
Database: PDB / ID: 8hjn
TitleCrystal structure of glycosyltransferase SgUGT94-289-3 in complex with UPG
Componentsglycosyltransferase
KeywordsTRANSFERASE / mogroside / UGT / Siraitia grosvenorii
Function / homologyURIDINE-5'-DIPHOSPHATE-GLUCOSE
Function and homology information
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, M. / Zhang, S. / Cui, S.
Funding support China, United Kingdom, 4items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)U20A2004 China
Chinese Academy of Sciences#YSBR-015 China
CAMS Innovation Fund for Medical Sciences (CIFMS)2021-I2M-1-071 United Kingdom
CitationJournal: To Be Published
Title: Structural insights into the catalytic selectivity of SgUGT94-289-3 towards mogrosides
Authors: Cui, S. / Zhang, S. / Wang, N. / Luo, Z. / Su, X. / Ma, X. / Li, M.
History
DepositionNov 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltransferase
B: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5214
Polymers102,3892
Non-polymers1,1332
Water00
1
A: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7612
Polymers51,1941
Non-polymers5661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area19510 Å2
MethodPISA
2
B: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7612
Polymers51,1941
Non-polymers5661
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.220, 80.095, 172.508
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 glycosyltransferase


Mass: 51194.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Production host: Escherichia coli (E. coli) / References: Transferases
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 43.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: Tris-HCl, polyethylene glycol 3350, NaCl, Polypropylene glycol P400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.2→72.65 Å / Num. obs: 13825 / % possible obs: 90.23 % / Redundancy: 7 % / Biso Wilson estimate: 63.24 Å2 / CC1/2: 0.988 / Net I/σ(I): 6.55
Reflection shellResolution: 3.2→3.315 Å / Num. unique obs: 1341 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
Blu-Ice1.18.2_3874data collection
PHENIX1.18.2_3874refinement
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JTD

6jtd


Resolution: 3.2→51.51 Å / SU ML: 0.3415 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.2293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277 718 5.21 %
Rwork0.2353 13061 -
obs0.2377 13779 90.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→51.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 72 0 6805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047018
X-RAY DIFFRACTIONf_angle_d0.96689536
X-RAY DIFFRACTIONf_chiral_restr0.05711050
X-RAY DIFFRACTIONf_plane_restr0.00731207
X-RAY DIFFRACTIONf_dihedral_angle_d20.01342574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.450.34631190.29992606X-RAY DIFFRACTION91.38
3.45-3.790.29671530.25442648X-RAY DIFFRACTION92.66
3.79-4.340.29081660.22612564X-RAY DIFFRACTION90.76
4.34-5.470.26821340.21882597X-RAY DIFFRACTION89.28
5.47-51.510.23661460.21632646X-RAY DIFFRACTION86.76

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