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- PDB-8k09: Pq3-O-UGT2 with 20(S)-Ginsenoside F2 -

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Basic information

Entry
Database: PDB / ID: 8k09
TitlePq3-O-UGT2 with 20(S)-Ginsenoside F2
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 (American ginseng)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å
AuthorsMei, K.R. / Ji, Q.S. / Liu, Y.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 / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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
C: Glycosyltransferase
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3464
Polymers101,7762
Non-polymers1,5702
Water00
1
C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6732
Polymers50,8881
Non-polymers7851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6732
Polymers50,8881
Non-polymers7851
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.270, 88.180, 164.510
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 (American ginseng) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0M4ME80, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-VEI / (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(3~{S},5~{R},8~{R},9~{R},10~{R},12~{R},13~{R},14~{R},17~{S})-17-[(2~{S})-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-methyl-hept-5-en-2-yl]-4,4,8,10,14-pentamethyl-12-oxidanyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol / ginsenoside F2


Mass: 785.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H72O13 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris pH5.13, 25% w/v Polyethylene glycol 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: Oct 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.36→49.76 Å / Num. obs: 13050 / % possible obs: 99.9 % / Redundancy: 11.9 % / CC1/2: 0.998 / Net I/σ(I): 13
Reflection shellResolution: 3.36→3.48 Å / Redundancy: 10.4 % / Num. unique obs: 2529 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
xia2data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36→37.27 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.95 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.3321 651 4.99 %
Rwork0.2964 --
obs0.2982 13050 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.36→37.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5993 0 110 0 6103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056230
X-RAY DIFFRACTIONf_angle_d0.8658445
X-RAY DIFFRACTIONf_dihedral_angle_d15.7242271
X-RAY DIFFRACTIONf_chiral_restr0.063977
X-RAY DIFFRACTIONf_plane_restr0.0051056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.620.43541330.3732400X-RAY DIFFRACTION100
3.62-3.980.4141190.35092467X-RAY DIFFRACTION100
3.98-4.560.38121330.31562444X-RAY DIFFRACTION100
4.56-5.740.37051290.31122479X-RAY DIFFRACTION100
5.74-37.270.2681370.25952609X-RAY DIFFRACTION100
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)
14.04330.23050.12993.89440.10768.1627-0.20410.00380.42650.2527-0.0890.14741.18040.76030.31881.03780.17250.23760.59520.13021.024319.4437-11.7642-1.2336
28.4972-4.53561.78028.6591-3.58155.4797-0.10120.1580.28720.4278-0.1227-0.5155-0.24250.40660.17230.6368-0.1188-0.00050.2526-0.16210.448213.8733-1.7881-18.2482
31.8116-1.4512-0.38585.5968-1.80234.14910.1873-0.20880.27951.0099-0.52571.55040.3769-2.04140.95550.98630.25210.13211.5733-0.21792.1274-11.85498.1045-9.787
46.4471-4.0248-3.33096.6921-2.22786.63950.14190.1091-0.66190.06330.21991.58070.8189-0.658-0.00420.6003-0.02190.1160.7663-0.0590.9829-2.85350.0063-20.6412
54.9454-3.59016.03253.7547-5.92681.9609-0.7146-0.02171.86321.0067-0.5171-0.01080.41222.8956-0.17261.50010.5159-0.10130.8996-0.4321.191426.2872-20.875-17.5186
65.6408-2.18043.5456.8733.75964.0737-1.1416-0.7785-0.36980.74590.7931-0.3243-0.1911-0.7922-0.00330.86050.25610.03340.9256-0.09990.418723.0662-19.6333-49.0283
79.2556-1.52781.57082.93841.59897.6192-0.6631-0.84720.63430.23360.2644-0.3250.00790.93830.39231.30810.3632-0.38410.7107-0.31961.136838.2693-2.2225-53.9676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 8 through 128 )
2X-RAY DIFFRACTION2chain 'C' and (resid 129 through 258 )
3X-RAY DIFFRACTION3chain 'C' and (resid 259 through 310 )
4X-RAY DIFFRACTION4chain 'C' and (resid 311 through 421 )
5X-RAY DIFFRACTION5chain 'C' and (resid 422 through 442 )
6X-RAY DIFFRACTION6chain 'A' and (resid 8 through 152 )
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 439 )

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