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- PDB-8wrk: glycosyltransferase UGT74AN3 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8wrk
Titleglycosyltransferase UGT74AN3
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Plant glycosyltransferase UGT74AN3
Function / homology
Function and homology information


quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / 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
PICEATANNOL / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsHuang, W. / Long, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Substrate Promiscuity, Crystal Structure, and Application of a Plant UDP-Glycosyltransferase UGT74AN3
Authors: Huang, W. / Zhang, X. / Li, J. / Lv, J. / Wang, Y. / He, Y. / Song, J. / Agren, H. / Jiang, R. / Deng, Z. / Long, F.
History
DepositionOct 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3233
Polymers52,6741
Non-polymers6482
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.673, 52.645, 200.340
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: 52674.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A385Z961, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL


Mass: 244.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, hanging drop / Details: 28% PEG2000MME, 0.2M KNO3, 0.1M Hepes pH 7.5

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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: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.03→44.53 Å / Num. obs: 32185 / % possible obs: 99.77 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 37.07
Reflection shellResolution: 2.031→2.103 Å / Num. unique obs: 3140 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→44.53 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 2000 6.23 %
Rwork0.1936 --
obs0.1963 32125 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 43 182 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073551
X-RAY DIFFRACTIONf_angle_d0.8974819
X-RAY DIFFRACTIONf_dihedral_angle_d7.477466
X-RAY DIFFRACTIONf_chiral_restr0.053553
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.30081380.21332088X-RAY DIFFRACTION98
2.08-2.140.26821400.19932099X-RAY DIFFRACTION100
2.14-2.20.24721420.19752148X-RAY DIFFRACTION100
2.2-2.270.22431390.19512089X-RAY DIFFRACTION100
2.27-2.350.24991410.19392117X-RAY DIFFRACTION100
2.35-2.450.22751410.19972138X-RAY DIFFRACTION100
2.45-2.560.26871420.20882136X-RAY DIFFRACTION100
2.56-2.690.29431430.20972152X-RAY DIFFRACTION100
2.69-2.860.28071420.21142135X-RAY DIFFRACTION100
2.86-3.080.26341420.21472147X-RAY DIFFRACTION100
3.08-3.390.25151440.20942158X-RAY DIFFRACTION100
3.39-3.880.20081440.1862189X-RAY DIFFRACTION100
3.88-4.890.18471480.15642205X-RAY DIFFRACTION100
4.89-44.530.23891540.19552324X-RAY DIFFRACTION99

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