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- PDB-9ksv: Complex structure of PcApiGT/UDP/Apigenin 7-O-glucoside -

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Basic information

Entry
Database: PDB / ID: 9ksv
TitleComplex structure of PcApiGT/UDP/Apigenin 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: 2.48 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)49,9263
Polymers49,0901
Non-polymers8372
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.160, 75.160, 162.810
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: 49089.688 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-A1EGT / Apigetrin / apigenin 7-O-beta-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.: 76 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging 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: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.48→36.62 Å / Num. obs: 19600 / % possible obs: 99.9 % / Redundancy: 19.1 % / CC1/2: 0.992 / Net I/σ(I): 10.7
Reflection shellResolution: 2.48→2.54 Å / Num. unique obs: 1440 / CC1/2: 0.738

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Processing

Software
NameVersionClassification
PHENIXPhenix1.20.1-4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→32.55 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 3612 9.97 %
Rwork0.2047 --
obs0.2109 19557 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→32.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 56 76 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093187
X-RAY DIFFRACTIONf_angle_d1.0174327
X-RAY DIFFRACTIONf_dihedral_angle_d8.251458
X-RAY DIFFRACTIONf_chiral_restr0.057502
X-RAY DIFFRACTIONf_plane_restr0.007544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.510.34671470.32741272X-RAY DIFFRACTION98
2.51-2.550.39731290.31831226X-RAY DIFFRACTION99
2.55-2.580.31571350.29731251X-RAY DIFFRACTION98
2.58-2.620.3791410.29871239X-RAY DIFFRACTION99
2.62-2.660.36691430.28731241X-RAY DIFFRACTION99
2.66-2.710.33471470.26431267X-RAY DIFFRACTION98
2.71-2.750.31431420.27241217X-RAY DIFFRACTION98
2.75-2.80.36571380.27811258X-RAY DIFFRACTION99
2.8-2.860.33081360.25911231X-RAY DIFFRACTION99
2.86-2.920.27461320.25981262X-RAY DIFFRACTION99
2.92-2.980.29311340.24931265X-RAY DIFFRACTION99
2.98-3.050.29691360.27051262X-RAY DIFFRACTION100
3.05-3.120.32271420.23231269X-RAY DIFFRACTION99
3.12-3.210.31281390.22971247X-RAY DIFFRACTION100
3.21-3.30.26291400.20111246X-RAY DIFFRACTION100
3.3-3.410.29321420.21011272X-RAY DIFFRACTION100
3.41-3.530.29351400.20181255X-RAY DIFFRACTION100
3.53-3.670.25111250.18291256X-RAY DIFFRACTION100
3.67-3.840.24461480.1871248X-RAY DIFFRACTION100
3.84-4.040.25941370.17541260X-RAY DIFFRACTION100
4.04-4.290.21811360.16141252X-RAY DIFFRACTION100
4.29-4.620.23571380.16161279X-RAY DIFFRACTION100
4.63-5.090.2271300.1621273X-RAY DIFFRACTION100
5.09-5.820.23271460.20181247X-RAY DIFFRACTION100
5.82-7.320.2561460.2111255X-RAY DIFFRACTION100
7.32-32.550.21521430.15761258X-RAY DIFFRACTION99

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