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- PDB-9ksx: Complex structure of CaApiGT/UDP/Quercetin 3-O-xyloside -

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Basic information

Entry
Database: PDB / ID: 9ksx
TitleComplex structure of CaApiGT/UDP/Quercetin 3-O-xyloside
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: 1.55 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
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9623
Polymers51,1241
Non-polymers8392
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.775, 117.950, 47.088
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: 51123.863 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-A1EGW / Quercetin 3-O-xyloside


Type: D-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.: 467 / 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: 43.23 %
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: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.55→117.95 Å / Num. obs: 65293 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.993 / Net I/σ(I): 9
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 9.7 % / Num. unique obs: 4763 / CC1/2: 0.215

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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: 1.55→47.42 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 3299 5.06 %
Rwork0.198 --
obs0.1993 65199 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3586 0 56 467 4109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083733
X-RAY DIFFRACTIONf_angle_d1.1025063
X-RAY DIFFRACTIONf_dihedral_angle_d6.452502
X-RAY DIFFRACTIONf_chiral_restr0.058564
X-RAY DIFFRACTIONf_plane_restr0.01639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.30921190.27682595X-RAY DIFFRACTION99
1.57-1.60.30911290.26982502X-RAY DIFFRACTION99
1.6-1.620.28751310.25792543X-RAY DIFFRACTION100
1.62-1.650.27741390.2532528X-RAY DIFFRACTION99
1.65-1.680.2781300.24512540X-RAY DIFFRACTION99
1.68-1.710.3041320.23912521X-RAY DIFFRACTION99
1.71-1.740.27511380.24052581X-RAY DIFFRACTION100
1.74-1.770.23671450.22962519X-RAY DIFFRACTION100
1.77-1.810.29121370.23952577X-RAY DIFFRACTION100
1.81-1.860.21541470.21022523X-RAY DIFFRACTION100
1.86-1.90.23391030.2172596X-RAY DIFFRACTION100
1.9-1.950.24761470.2192555X-RAY DIFFRACTION100
1.95-2.010.25371300.21082555X-RAY DIFFRACTION100
2.01-2.080.21781130.20212594X-RAY DIFFRACTION100
2.08-2.150.25621290.19792601X-RAY DIFFRACTION100
2.15-2.240.21561680.19622538X-RAY DIFFRACTION100
2.24-2.340.23471200.19262603X-RAY DIFFRACTION100
2.34-2.460.24391670.19732561X-RAY DIFFRACTION100
2.46-2.610.21611210.20232612X-RAY DIFFRACTION100
2.61-2.820.21541320.19632605X-RAY DIFFRACTION100
2.82-3.10.21511430.18512606X-RAY DIFFRACTION100
3.1-3.550.20811440.17512623X-RAY DIFFRACTION100
3.55-4.470.16011540.14792651X-RAY DIFFRACTION100
4.47-47.420.19781810.18352771X-RAY DIFFRACTION100

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