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- PDB-8j2v: Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin -

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Basic information

Entry
Database: PDB / ID: 8j2v
TitleGlucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glucosyl transferase
Function / homologyUDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / 7-hydroxy-6-methoxy-2H-1-benzopyran-2-one / Glycosyltransferase
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2343
Polymers53,9461
Non-polymers2882
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-15 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.580, 103.660, 54.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

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Components

#1: Protein Glycosyltransferase /


Mass: 53945.941 Da / Num. of mol.: 1
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 / Scopoletin


Mass: 192.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 30 % w/v PEG 5000 MME

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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: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→47.94 Å / Num. obs: 31435 / % possible obs: 96.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / Net I/σ(I): 19.02
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2558 / CC1/2: 0.621

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.94 Å / SU B: 11.591 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.169
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1576 5 %RANDOM
Rwork0.189 ---
obs0.191 29930 96.6 %-
Displacement parametersBiso mean: 53.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1.83 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 19 110 3871
LS refinement shellResolution: 2→2.048 Å
RfactorNum. reflection% reflection
Rfree0.334 89 -
Rwork0.372 --
obs-1693 75.93 %

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