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

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Basic information

Entry
Database: PDB / ID: 9ufi
TitleCrystal structure of a PhGs rhamnosyltransferase UGT79G15 from Rehmannia glutinosa in complex with UDP and FSA
ComponentsUGT79G15
KeywordsTRANSFERASE / catalysis
Function / homology: / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesRehmannia glutinosa (Chinese foxglove)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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)103,8856
Polymers101,8272
Non-polymers2,0574
Water2,252125
1
A: UGT79G15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9423
Polymers50,9141
Non-polymers1,0292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-6 kcal/mol
Surface area19150 Å2
MethodPISA
2
B: UGT79G15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9423
Polymers50,9141
Non-polymers1,0292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-8 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.105, 73.244, 134.294
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: 50913.602 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-A1EO9 / Forsythiaside A / [(2R,3S,4R,5R,6R)-6-[2-[3,4-bis(oxidanyl)phenyl]ethoxy]-2-[[(2R,3R,4R,5R,6S)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-4,5-bis(oxidanyl)oxan-3-yl] (E)-3-[3,4-bis(oxidanyl)phenyl]prop-2-enoate


Mass: 624.587 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C29H36O15
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
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: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→49.26 Å / Num. obs: 49883 / % possible obs: 98.56 % / Redundancy: 14.87 % / Biso Wilson estimate: 51.6 Å2 / CC1/2: 0.996 / Net I/σ(I): 56
Reflection shellResolution: 2.12→2.19 Å / Num. unique obs: 4995 / CC1/2: 0.652

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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: 2.12→49.26 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 29.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 2487 4.99 %
Rwork0.1996 --
obs0.2021 49883 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 88 125 7325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.115
X-RAY DIFFRACTIONf_dihedral_angle_d8.856964
X-RAY DIFFRACTIONf_chiral_restr0.0631112
X-RAY DIFFRACTIONf_plane_restr0.0091274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.190.33282510.32554732X-RAY DIFFRACTION99
2.19-2.280.4952120.42384261X-RAY DIFFRACTION89
2.28-2.390.3372410.28294764X-RAY DIFFRACTION100
2.39-2.510.30812570.25784776X-RAY DIFFRACTION100
2.51-2.670.31122520.23714778X-RAY DIFFRACTION100
2.67-2.870.28552490.23524817X-RAY DIFFRACTION100
2.87-3.160.30252550.2424767X-RAY DIFFRACTION100
3.16-3.620.27652590.20794813X-RAY DIFFRACTION100
3.62-4.560.20792560.15764810X-RAY DIFFRACTION99
4.56-49.260.18712550.15754878X-RAY DIFFRACTION99

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