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- PDB-9j9k: Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin a... -

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Basic information

Entry
Database: PDB / ID: 9j9k
TitleGlucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2F glucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glucosyl transferase / scopoletin / UDP glucose
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
7-hydroxy-6-methoxy-2H-1-benzopyran-2-one / Chem-U2F / Glycosyltransferase
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: Nat Commun / Year: 2025
Title: beta-Carotene alleviates substrate inhibition caused by asymmetric cooperativity.
Authors: Liao, J. / Shahul Hameed, U.F. / Hoffmann, T.D. / Kurze, E. / Sun, G. / Steinchen, W. / Nicoli, A. / Di Pizio, A. / Kuttler, C. / Song, C. / Catici, D.A.M. / Assaad-Gerbert, F. / Hoffmann, T. ...Authors: Liao, J. / Shahul Hameed, U.F. / Hoffmann, T.D. / Kurze, E. / Sun, G. / Steinchen, W. / Nicoli, A. / Di Pizio, A. / Kuttler, C. / Song, C. / Catici, D.A.M. / Assaad-Gerbert, F. / Hoffmann, T. / Arold, S.T. / Schwab, W.G.
History
DepositionAug 22, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 4, 2024ID: 8J2T
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0976
Polymers106,5762
Non-polymers1,5214
Water00
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0493
Polymers53,2881
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0493
Polymers53,2881
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.607, 114.919, 104.249
Angle α, β, γ (deg.)90.00, 103.12, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Glycosyltransferase


Mass: 53288.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana benthamiana (plant)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8K1ZRH3, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-T83 / 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one


Mass: 192.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / 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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30% w/vPEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.15→46.83 Å / Num. obs: 19895 / % possible obs: 97.5 % / Redundancy: 6.9 % / CC1/2: 0.99 / Net I/σ(I): 5.2
Reflection shellResolution: 3.15→3.26 Å / Num. unique obs: 3327 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
REFMACRefmac5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8J2V

8j2v


Resolution: 3.15→46.83 Å / SU B: 57.872 / SU ML: 0.444 / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25828 901 4.5 %RANDOM
Rwork0.18953 ---
obs0.1925 18992 98.24 %-
Displacement parametersBiso mean: 78.474 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20.42 Å2
2---3.8 Å2-0 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 3.15→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7393 0 100 0 7493
LS refinement shellResolution: 3.15→3.26 Å
RfactorNum. reflection% reflection
Rfree0.34 --
Rwork0.33 1694 -
obs--83.78 %

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