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- PDB-9kt0: Complex structure of PcApiGT/UDP/Genistein 7-O-glucoside -

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Basic information

Entry
Database: PDB / ID: 9kt0
TitleComplex structure of PcApiGT/UDP/Genistein 7-O-glucoside
ComponentsPcApiGT
KeywordsPLANT PROTEIN / glycosyltransferase / apiosyltransferase
Function / homology: / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesPetroselinum crispum (parsley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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

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Assembly

Deposited unit
A: PcApiGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9403
Polymers49,1041
Non-polymers8372
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.230, 75.230, 161.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PcApiGT


Mass: 49103.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petroselinum crispum (parsley) / Production host: Escherichia coli (E. coli)
#2: Sugar ChemComp-A1EGY / Genistin / Genistein 7-O-glucoside


Type: D-saccharide / Mass: 432.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20O10 / 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.: 16 / 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: 2.69 Å3/Da / Density % sol: 54.25 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 25% w/v polyethylene glycol 3,350, 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.17→65.15 Å / Num. obs: 28864 / % possible obs: 100 % / Redundancy: 19.8 % / CC1/2: 0.999 / Net I/σ(I): 9.3
Reflection shellResolution: 2.17→2.29 Å / Num. unique obs: 4141 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→32.58 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 45.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2977 1316 4.76 %
Rwork0.2565 --
obs0.2585 27626 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.17→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 56 16 3193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093245
X-RAY DIFFRACTIONf_angle_d1.0484413
X-RAY DIFFRACTIONf_dihedral_angle_d7.645469
X-RAY DIFFRACTIONf_chiral_restr0.058517
X-RAY DIFFRACTIONf_plane_restr0.008553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.260.49541210.47692009X-RAY DIFFRACTION68
2.26-2.360.47121450.43812918X-RAY DIFFRACTION97
2.36-2.480.40431510.39272952X-RAY DIFFRACTION99
2.48-2.640.39151600.34412971X-RAY DIFFRACTION100
2.64-2.840.43171420.32743047X-RAY DIFFRACTION100
2.84-3.130.36421280.30933051X-RAY DIFFRACTION100
3.13-3.580.30391500.28093041X-RAY DIFFRACTION100
3.58-4.510.28061440.22433099X-RAY DIFFRACTION100
4.51-32.580.2291750.19313222X-RAY DIFFRACTION100

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