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- PDB-8jzq: Crystal structure of Panax quinquefolius Pq3-O-UGT2 -

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Basic information

Entry
Database: PDB / ID: 8jzq
TitleCrystal structure of Panax quinquefolius Pq3-O-UGT2
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltranferase / GT-B fold
Function / homologycarbohydrate derivative biosynthetic process / UDP-glycosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / terpenoid biosynthetic process / Transferases; Glycosyltransferases; Hexosyltransferases / Glycosyltransferase
Function and homology information
Biological speciesPanax quinquefolius (American ginseng)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsMei, K. / Ji, Q. / Liu, Y.
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 6, 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
A: Glycosyltransferase
B: Glycosyltransferase
C: Glycosyltransferase
D: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)203,5524
Polymers203,5524
Non-polymers00
Water00
1
A: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)50,8881
Polymers50,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)50,8881
Polymers50,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)50,8881
Polymers50,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)50,8881
Polymers50,8881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.987, 80.886, 126.377
Angle α, β, γ (deg.)93.96, 90.00, 93.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glycosyltransferase


Mass: 50888.051 Da / Num. of mol.: 4
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
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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.25 M ammonium acetate, 0.2 M Sodium citrate tribasic dihydrate, pH 5.0, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 39238 / % possible obs: 95 % / Redundancy: 2.8 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.091 / Rrim(I) all: 0.16 / Χ2: 1.143 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.90.74720100.5430.8390.4950.8990.86695.8
2.95-32.80.65919580.4960.8140.4470.80.89395.8
3-3.062.80.52919420.5510.8430.3560.640.93595.2
3.06-3.122.70.43819870.650.8880.3060.5371.0193.8
3.12-3.192.70.43318630.7050.9090.30.5291.0193.5
3.19-3.272.90.34520150.7910.940.230.4161.08296.8
3.27-3.3530.27620440.8540.960.1840.3331.16797
3.35-3.442.90.34219200.9460.9860.2430.4221.34293.2
3.44-3.542.90.30418950.9340.9830.2160.3751.35992.8
3.54-3.652.90.25320120.9550.9880.1710.3071.10595.9
3.65-3.782.80.19318590.9680.9920.1370.2381.22292.5
3.78-3.942.70.17119110.9680.9920.1250.2141.33491.3
3.94-4.112.60.11419240.9660.9910.0810.1411.12394.3
4.11-4.332.80.09520010.9780.9940.0660.1171.2596.1
4.33-4.62.90.09120080.9730.9930.0620.1111.21196.9
4.6-4.962.90.08619750.9790.9950.0590.1041.19696.9
4.96-5.462.90.08620000.9780.9940.0590.1051.25496.6
5.46-6.242.70.08319580.9910.9980.0590.1021.21795.1
6.24-7.8630.07120390.980.9950.0480.0861.16897.2
7.86-502.80.05219170.9910.9980.0370.0651.12793.5

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→37.7 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3329 1922 4.92 %
Rwork0.3073 --
obs0.3086 39084 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11872 0 0 0 11872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812108
X-RAY DIFFRACTIONf_angle_d1.22116344
X-RAY DIFFRACTIONf_dihedral_angle_d13.5494484
X-RAY DIFFRACTIONf_chiral_restr0.0721844
X-RAY DIFFRACTIONf_plane_restr0.0082088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.41551240.33092583X-RAY DIFFRACTION90
2.96-3.040.35281210.32842640X-RAY DIFFRACTION95
3.04-3.130.34981300.34082697X-RAY DIFFRACTION93
3.13-3.230.37831300.3442657X-RAY DIFFRACTION95
3.23-3.350.34961360.32252776X-RAY DIFFRACTION97
3.35-3.480.44941510.40032479X-RAY DIFFRACTION90
3.48-3.640.36731670.33972729X-RAY DIFFRACTION97
3.64-3.830.3761260.35472584X-RAY DIFFRACTION92
3.83-4.070.3771270.31912568X-RAY DIFFRACTION91
4.07-4.390.32441210.27922706X-RAY DIFFRACTION96
4.39-4.830.27941550.2782716X-RAY DIFFRACTION97
4.83-5.530.32311550.28972683X-RAY DIFFRACTION97
5.53-6.950.34021520.31332687X-RAY DIFFRACTION96
6.95-37.70.23941270.25452657X-RAY DIFFRACTION94

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