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- PDB-9imi: Crystal structure of UGT94BY1 in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 9imi
TitleCrystal structure of UGT94BY1 in complex with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / triterpenoid / glycosyltransferase / catalytic mechanism
Function / homologycarbohydrate derivative biosynthetic process / UDP-glycosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesPlatycodon grandiflorus (balloon flower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJiang, Z. / Yuan, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173926 China
CitationJournal: To Be Published
Title: Functional Characterization and Structure Basis Provide Molecular Mechanisms of UGT94BY1 for Branched-Chain Glycoside Biosynthesis
Authors: Jiang, Z. / Yuan, Y.
History
DepositionJul 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 9, 2025Provider: 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)53,0862
Polymers52,6821
Non-polymers4041
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-9 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.470, 71.469, 102.488
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: 52681.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platycodon grandiflorus (balloon flower)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A9Y1LBL2, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20%(W/V)PEG3350,200mM Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→58.62 Å / Num. obs: 31115 / % possible obs: 90.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.892 / Num. unique obs: 3376

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.18 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1505 4.85 %
Rwork0.1951 --
obs0.1971 31024 90.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 25 142 3560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083502
X-RAY DIFFRACTIONf_angle_d0.9064734
X-RAY DIFFRACTIONf_dihedral_angle_d5.727453
X-RAY DIFFRACTIONf_chiral_restr0.053531
X-RAY DIFFRACTIONf_plane_restr0.008590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.37311080.29382324X-RAY DIFFRACTION98
2.09-2.140.2762980.24892013X-RAY DIFFRACTION98
2.14-2.230.24941410.20142919X-RAY DIFFRACTION100
2.23-2.330.27331500.21012575X-RAY DIFFRACTION89
2.33-2.450.27621460.20632928X-RAY DIFFRACTION100
2.45-2.60.27271540.21032911X-RAY DIFFRACTION100
2.6-2.80.32611110.2292226X-RAY DIFFRACTION76
2.8-3.080.24671540.21722945X-RAY DIFFRACTION100
3.09-3.530.24771530.20382966X-RAY DIFFRACTION100
3.53-4.450.20661280.16872595X-RAY DIFFRACTION87
4.45-28.180.19881620.17583117X-RAY DIFFRACTION100

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