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- PDB-8k08: Pq3-O-UGT2 with 20(S)-Ginsenoside Rh2 -

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Basic information

Entry
Database: PDB / ID: 8k08
TitlePq3-O-UGT2 with 20(S)-Ginsenoside Rh2
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosytransferase
Function / homology
Function and homology information


carbohydrate derivative biosynthetic process / UDP-glycosyltransferase activity / terpenoid biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
: / Glycosyltransferase
Similarity search - Component
Biological speciesPanax quinquefolius (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJi, Q.S. / Liu, Y.R. / Mei, K.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2025
Title: Structural Insights into the Substrate Recognition of Ginsenoside Glycosyltransferase Pq3-O-UGT2.
Authors: Ji, Q. / Liu, Y. / Zhang, H. / Gao, Y. / Ding, Y. / Ding, Y. / Xie, J. / Zhang, J. / Jin, X. / Lai, B. / Chen, C. / Wang, J. / Gao, W. / Mei, K.
History
DepositionJul 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0224
Polymers101,7762
Non-polymers1,2462
Water00
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5112
Polymers50,8881
Non-polymers6231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5112
Polymers50,8881
Non-polymers6231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.349, 90.203, 155.873
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: 50888.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Panax quinquefolius (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M4ME80, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-8YG / Ginsenoside Rh2 / (2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-[[(3S,5R,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17-[(2S)-6-methyl-2-oxidanyl-hept-5-en-2-yl]-12-oxidanyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol


Mass: 622.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H62O8 / Feature type: SUBJECT OF INVESTIGATION
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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2.0 M sodium chloride, 0.2 M sodium citrate, pH 5.2, 25% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.19→52.26 Å / Num. obs: 16348 / % possible obs: 95.3 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 3.19→3.3 Å / Num. unique obs: 1655 / CC1/2: 0.331

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→52.26 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3204 573 4.68 %
Rwork0.293 --
obs0.2944 12245 93.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 88 0 6329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036461
X-RAY DIFFRACTIONf_angle_d0.6668754
X-RAY DIFFRACTIONf_dihedral_angle_d14.2892380
X-RAY DIFFRACTIONf_chiral_restr0.0491002
X-RAY DIFFRACTIONf_plane_restr0.0051103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.850.4221200.39022394X-RAY DIFFRACTION79
3.85-4.410.40641410.35143052X-RAY DIFFRACTION99
4.41-5.550.34331480.29413046X-RAY DIFFRACTION99
5.55-52.260.26321640.25253180X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4744-0.3412-0.04773.6574-0.15372.5709-0.44530.4422-0.93780.14860.03870.14670.09080.51160.40070.95030.17550.18910.82080.00480.8469-34.6612-23.834833.3738
22.16541.2012-0.35113.854-1.63972.9240.35380.49550.82440.1772-0.08080.5239-0.01890.1453-0.14540.91850.019-0.01460.76280.0260.7601-34.4604-5.151125.3563
32.0444-1.10660.34442.5319-0.28964.722-0.45380.78650.7005-0.524-0.6634-0.09580.21351.14570.90820.9617-0.145-0.01651.3470.13991.0816-6.399-7.632517.7671
45.59510.7155-0.73883.47060.95682.815-0.72480.5722-0.18860.3720.1232-0.7782-0.06891.19660.61161.09390.0511-0.07461.28990.05850.9919-13.7056-5.077424.4479
53.487-0.1145-1.71791.5891-0.11241.27110.05610.06790.97420.66610.1896-0.4559-0.94660.1613-0.18961.2274-0.1823-0.07141.0132-0.12381.0803-23.85571.140530.0416
64.01740.1294-0.32392.6391.94145.5114-0.6345-0.3621-0.3358-0.21160.07160.4479-0.3892-0.12410.60230.7860.1542-0.0980.7721-0.02080.9017-53.22369.8661-1.2831
73.2271-0.5036-1.35392.44511.20482.1228-0.14490.0347-0.1898-0.04090.063-0.51030.21070.39950.12480.78260.1388-0.09790.79510.1240.8773-38.05161.4881-17.6591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 247 )
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 302 )
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 369 )
5X-RAY DIFFRACTION5chain 'A' and (resid 370 through 442 )
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 152 )
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 442 )

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