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

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Basic information

Entry
Database: PDB / ID: 9lrj
TitleGlucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2Fglucose in the presence of retinol
ComponentsGlycosyltransferase
KeywordsHYDROLASE / Glycosyl transferase / Scopoletin / Beta carotene
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: 3.11 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technlogy 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
DepositionJan 31, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionFeb 12, 2025ID: 9J9C
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
C: Glycosyltransferase
D: Glycosyltransferase
E: Glycosyltransferase
F: Glycosyltransferase
G: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,22719
Polymers375,2887
Non-polymers4,93912
Water00
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3733
Polymers53,6131
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3733
Polymers53,6131
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3733
Polymers53,6131
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3733
Polymers53,6131
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1812
Polymers53,6131
Non-polymers5681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3733
Polymers53,6131
Non-polymers7602
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1812
Polymers53,6131
Non-polymers5681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.716, 171.782, 153.378
Angle α, β, γ (deg.)90.00, 93.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycosyltransferase


Mass: 53612.574 Da / Num. of mol.: 7
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-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-T83 / 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one


Mass: 192.168 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H8O4 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate pH 6.5, 15% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98013 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: 0.98013 Å / Relative weight: 1
ReflectionResolution: 3.11→48.89 Å / Num. obs: 56153 / % possible obs: 91.9 % / Redundancy: 6.6 % / CC1/2: 0.97 / Net I/σ(I): 7
Reflection shellResolution: 3.11→3.56 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3742 / CC1/2: 0.39 / % possible all: 54.5

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Processing

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

8j2v


Resolution: 3.11→48.89 Å / Cross valid method: THROUGHOUT / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31216 2878 5.1 %RANDOM
Rwork0.26843 ---
obs0.27064 53275 68.76 %-
Displacement parametersBiso mean: 33.393 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0 Å21.89 Å2
2---0.71 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 3.11→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25419 0 322 0 25741
LS refinement shellResolution: 3.11→3.56 Å /
RfactorNum. reflection
Rfree0.41 -
Rwork0.37 -
obs-3560

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