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- PDB-9uei: Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Re... -

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Basic information

Entry
Database: PDB / ID: 9uei
TitleCrystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa
ComponentsUGT79G15
KeywordsTRANSFERASE / catalysis
Biological speciesRehmannia glutinosa (Chinese foxglove)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWei, H.L. / Liu, W.D. / Zhuang, Y.B. / Liu, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant Commun. / Year: 2025
Title: Structural insights into the catalytic mechanism of the phenylethanoid glycoside rhamnosyltransferase UGT79G15 from Rehmannia glutinosa.
Authors: Ma, R. / Wei, H. / Zhuang, Y. / Wu, Y. / Li, Z. / Chen, Y. / Huang, J. / Yan, X. / Liu, W. / Liu, T.
History
DepositionApr 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UGT79G15
B: UGT79G15


Theoretical massNumber of molelcules
Total (without water)100,8182
Polymers100,8182
Non-polymers00
Water17,511972
1
A: UGT79G15


Theoretical massNumber of molelcules
Total (without water)50,4091
Polymers50,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UGT79G15


Theoretical massNumber of molelcules
Total (without water)50,4091
Polymers50,4091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.745, 71.970, 133.890
Angle α, β, γ (deg.)90.00, 97.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UGT79G15


Mass: 50409.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rehmannia glutinosa (Chinese foxglove)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0. 4 M NaNO3,30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→44.37 Å / Num. obs: 75916 / % possible obs: 99.49 % / Redundancy: 4.5 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Χ2: 0.62 / Net I/σ(I): 2.28
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.041 / Num. unique obs: 2486 / CC1/2: 0.765 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→44.37 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 3789 4.99 %
Rwork0.1902 --
obs0.1919 75872 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7052 0 0 972 8024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.922
X-RAY DIFFRACTIONf_dihedral_angle_d10.355952
X-RAY DIFFRACTIONf_chiral_restr0.1261085
X-RAY DIFFRACTIONf_plane_restr0.0121265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.950.2783720.23467273X-RAY DIFFRACTION100
1.95-2.030.27183810.22167139X-RAY DIFFRACTION100
2.03-2.120.2313770.19577201X-RAY DIFFRACTION100
2.12-2.230.23583790.19227200X-RAY DIFFRACTION100
2.23-2.370.23133770.19187220X-RAY DIFFRACTION100
2.37-2.550.24033710.19327152X-RAY DIFFRACTION100
2.55-2.810.23183960.19167224X-RAY DIFFRACTION100
2.81-3.220.22633720.19617182X-RAY DIFFRACTION99
3.22-4.050.21293810.17737184X-RAY DIFFRACTION99
4.05-44.370.19473830.17877308X-RAY DIFFRACTION99

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