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- PDB-8yp7: Crystal structure of glucosyltransferase RrUGT3 -

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Basic information

Entry
Database: PDB / ID: 8yp7
TitleCrystal structure of glucosyltransferase RrUGT3
ComponentsGlycosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / uridine diphosphate glucosyltransferases / glycosylation / regioselectivity
Function / homologyUDP-glycosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / Glycosyltransferase
Function and homology information
Biological speciesRhodiola rosea (rose-root)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsCai, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200030 China
CitationJournal: To Be Published
Title: Crystal structure of glucosyltransferase RrUGT3
Authors: Cai, Y.
History
DepositionMar 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)52,0931
Polymers52,0931
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.191, 70.826, 92.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyltransferase


Mass: 52093.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodiola rosea (rose-root) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2I6B3N5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Citric acid, 0.05 M BIS-TRIS propane, pH 4.5, 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.87→46.37 Å / Num. obs: 38051 / % possible obs: 99.2 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.026 / Rrim(I) all: 0.093 / Χ2: 0.99 / Net I/σ(I): 20.6
Reflection shellResolution: 1.87→1.91 Å / % possible obs: 87.6 % / Redundancy: 13.2 % / Rmerge(I) obs: 2.018 / Num. measured all: 27957 / Num. unique obs: 2124 / CC1/2: 0.585 / Rpim(I) all: 0.572 / Rrim(I) all: 2.099 / Χ2: 0.98 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→46.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.118 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21208 1865 4.9 %RANDOM
Rwork0.17948 ---
obs0.18112 36124 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.927 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.87→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 0 160 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173260
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.6324762
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5657575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31722.405158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7611518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02699
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5932.9611776
X-RAY DIFFRACTIONr_mcbond_other2.5912.961775
X-RAY DIFFRACTIONr_mcangle_it3.5344.422213
X-RAY DIFFRACTIONr_mcangle_other3.5344.422214
X-RAY DIFFRACTIONr_scbond_it3.7173.4131724
X-RAY DIFFRACTIONr_scbond_other3.7163.4131725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.584.9422550
X-RAY DIFFRACTIONr_long_range_B_refined6.72735.9393866
X-RAY DIFFRACTIONr_long_range_B_other6.71335.8533849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.875→1.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 154 -
Rwork0.363 2579 -
obs--98.95 %

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