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- PDB-8j2t: Glucosyl Transferase NbUGT72AY1 co-crystallized with UDP-2F gluco... -

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Basic information

Entry
Database: PDB / ID: 8j2t
TitleGlucosyl Transferase NbUGT72AY1 co-crystallized with UDP-2F glucose and Scopoletin
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glucosyl transferase
Function / homologyUDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycosyltransferase
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
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: To Be Published
Title: Glucosyl Transferase NbUGT72AY1 co-crystallized with UDP-2F glucose and Scopoletin
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionApr 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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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)109,4096
Polymers107,8922
Non-polymers1,5174
Water00
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7043
Polymers53,9461
Non-polymers7582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area19430 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7043
Polymers53,9461
Non-polymers7582
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20750 Å2
MethodPISA
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: 53945.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8K1ZRH3
#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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 MLithium 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: 3.08→46.9 Å / Num. obs: 18992 / % possible obs: 97.2 % / Redundancy: 3.6 % / CC1/2: 0.984 / Net I/σ(I): 4.9
Reflection shellResolution: 3.08→3.16 Å / Num. unique obs: 3327 / CC1/2: 0.464

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.83 Å / SU B: 27.782 / SU ML: 0.454 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 901 4.5 %RANDOM
Rwork0.197 ---
obs0.2 18992 98.2 %-
Displacement parametersBiso mean: 77.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.06 Å2
2--0.14 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.15→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7516 0 100 0 7616
LS refinement shellResolution: 3.152→3.234 Å
RfactorNum. reflection% reflection
Rfree0.39 53 -
Rwork0.351 --
obs-1107 77.9 %

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