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- PDB-8wrj: glycosyltransferase UGT74AN3 -

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Basic information

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


UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
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
Chem-6JI / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)54,3613
Polymers53,5721
Non-polymers7892
Water4,125229
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)46.022, 53.005, 200.795
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: 53572.391 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-6JI / 5-[(1R,2S,4R,6R,7R,10S,11S,14S,16R)-14-hydroxy-7,11-dimethyl-3-oxapentacyclo[8.8.0.02,4.02,7.011,16]octadecan-6-yl]pyran-2-one / Resibufogenin


Mass: 384.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O4 / 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.: 229 / 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: 46.19 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, hanging drop / Details: 28% PEG200MME, 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: NFPSS / 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: 1.85→46.87 Å / Num. obs: 42636 / % possible obs: 99.3 % / Redundancy: 12.2 % / CC1/2: 0.999 / Net I/σ(I): 19.7
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 2409 / CC1/2: 0.84

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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: 1.85→44.86 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 2121 4.99 %
Rwork0.2091 --
obs0.2112 42535 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 53 229 3664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083518
X-RAY DIFFRACTIONf_angle_d0.9814783
X-RAY DIFFRACTIONf_dihedral_angle_d8.604474
X-RAY DIFFRACTIONf_chiral_restr0.058557
X-RAY DIFFRACTIONf_plane_restr0.006589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.36251390.30872465X-RAY DIFFRACTION92
1.9-1.940.34791340.2692557X-RAY DIFFRACTION97
1.94-20.29691480.24272683X-RAY DIFFRACTION100
2-2.050.26921350.22782644X-RAY DIFFRACTION100
2.05-2.120.25111330.22252707X-RAY DIFFRACTION100
2.12-2.20.26251400.22482683X-RAY DIFFRACTION100
2.2-2.280.26061520.21512652X-RAY DIFFRACTION100
2.28-2.390.27931390.22682700X-RAY DIFFRACTION100
2.39-2.510.26931460.22282702X-RAY DIFFRACTION100
2.51-2.670.28231400.232702X-RAY DIFFRACTION100
2.67-2.880.26961310.23022735X-RAY DIFFRACTION100
2.88-3.170.291280.22222730X-RAY DIFFRACTION100
3.17-3.620.23121590.20622725X-RAY DIFFRACTION100
3.63-4.570.22681440.16942790X-RAY DIFFRACTION100
4.57-44.860.21171530.19052939X-RAY DIFFRACTION100

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