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- PDB-9uf7: Crystal structure of a PhGs rhamnosyltransferase UGT79G15 from Re... -

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Basic information

Entry
Database: PDB / ID: 9uf7
TitleCrystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP
ComponentsUGT79G15
KeywordsTRANSFERASE / catalysis
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesRehmannia glutinosa (Chinese foxglove)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UGT79G15
B: UGT79G15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3684
Polymers100,5602
Non-polymers8082
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-7 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.254, 72.059, 134.360
Angle α, β, γ (deg.)90.00, 97.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UGT79G15


Mass: 50279.887 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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
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: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.4→48.89 Å / Num. obs: 34485 / % possible obs: 99.93 % / Redundancy: 4.09 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.981 / Net I/σ(I): 1.91
Reflection shellResolution: 2.4→2.48 Å / Num. unique obs: 3402 / CC1/2: 0.591

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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: 2.4→48.89 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.72 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1717 4.98 %
Rwork0.206 --
obs0.208 34485 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 50 186 7283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.279
X-RAY DIFFRACTIONf_dihedral_angle_d6.394952
X-RAY DIFFRACTIONf_chiral_restr0.0571092
X-RAY DIFFRACTIONf_plane_restr0.0171266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.30941730.26323234X-RAY DIFFRACTION100
2.48-2.580.35781710.25413270X-RAY DIFFRACTION100
2.58-2.70.3161670.2333240X-RAY DIFFRACTION100
2.7-2.840.28361650.23883269X-RAY DIFFRACTION100
2.84-3.020.29261730.23843257X-RAY DIFFRACTION100
3.02-3.250.26061740.22293270X-RAY DIFFRACTION100
3.25-3.580.25711740.20713301X-RAY DIFFRACTION100
3.58-4.10.22081720.17993264X-RAY DIFFRACTION100
4.1-5.160.1741700.16633302X-RAY DIFFRACTION100
5.17-48.890.23551780.19393361X-RAY DIFFRACTION100

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