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- PDB-9ksy: Complex structure of CaApiGT/UDP/Guaijaverin -

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Basic information

Entry
Database: PDB / ID: 9ksy
TitleComplex structure of CaApiGT/UDP/Guaijaverin
ComponentsUDP-glycosyltransferase 79B30-like
KeywordsPLANT PROTEIN / glycosyltransferase / apiosyltransferase
Function / homology: / UDP-glucosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / : / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 79B30-like
Function and homology information
Biological speciesCicer arietinum (chickpea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsWang, H.T. / Wang, Z.L. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Insights into the Mechanisms of Sugar Acceptor Selectivity of Plant Flavonoid Apiosyltransferases.
Authors: Wang, H.T. / Wang, Z.L. / Chen, N.H. / Huang, W. / Zou, J.L. / Tian, Y.G. / Ye, G. / Huang, J. / Wu, R. / Ye, M.
History
DepositionNov 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glycosyltransferase 79B30-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3933
Polymers51,5541
Non-polymers8392
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.557, 119.461, 47.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein UDP-glycosyltransferase 79B30-like / UGT79B91


Mass: 51554.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cicer arietinum (chickpea) / Gene: LOC101505166 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S2XDD2
#2: Sugar ChemComp-A1EGX / Guaijaverin


Type: L-saccharide / Mass: 434.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18O11 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.17 Å3/Da / Density % sol: 43.42 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% w/v polyethylene glycol 3350, 0.2 M Calcium acetate hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.66→118.71 Å / Num. obs: 54000 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.974 / Net I/σ(I): 7
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 12.3 % / Num. unique obs: 3930 / CC1/2: 0.247 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→30.7 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 2213 4.91 %
Rwork0.1878 --
obs0.1901 45026 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.77→30.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 56 359 4015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.985
X-RAY DIFFRACTIONf_dihedral_angle_d7.627521
X-RAY DIFFRACTIONf_chiral_restr0.06567
X-RAY DIFFRACTIONf_plane_restr0.009642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.3511230.26282370X-RAY DIFFRACTION89
1.81-1.850.29271130.25332545X-RAY DIFFRACTION96
1.85-1.90.29731510.22792679X-RAY DIFFRACTION99
1.9-1.950.25691210.22872655X-RAY DIFFRACTION100
1.95-20.26111370.21432660X-RAY DIFFRACTION100
2-2.070.25031540.20342673X-RAY DIFFRACTION100
2.07-2.140.28641400.19462648X-RAY DIFFRACTION100
2.14-2.230.23351350.19332680X-RAY DIFFRACTION100
2.23-2.330.30331370.19462689X-RAY DIFFRACTION100
2.33-2.450.22091280.20012697X-RAY DIFFRACTION100
2.45-2.610.23411540.19242691X-RAY DIFFRACTION100
2.61-2.810.25141380.19652701X-RAY DIFFRACTION100
2.81-3.090.21711410.18632709X-RAY DIFFRACTION100
3.09-3.540.2441410.17882737X-RAY DIFFRACTION100
3.54-4.450.18881310.14722792X-RAY DIFFRACTION100
4.45-30.70.18731690.16822887X-RAY DIFFRACTION100

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