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- PDB-9ksz: Complex structure of PcApiGT/UDP -

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Basic information

Entry
Database: PDB / ID: 9ksz
TitleComplex structure of PcApiGT/UDP
ComponentsPcApiGT
KeywordsPLANT PROTEIN / glycosyltransferase / apiosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesPetroselinum crispum (parsley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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)49,4942
Polymers49,0901
Non-polymers4041
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-9 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.779, 75.779, 164.505
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: 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.: 106 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 25% w/v polyethylene glycol 3350, 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
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.65→42.08 Å / Num. obs: 16517 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.03 / Rrim(I) all: 0.105 / Χ2: 1.03 / Net I/σ(I): 17 / Num. measured all: 201440
Reflection shellResolution: 2.65→2.78 Å / % possible obs: 99.2 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.83 / Num. measured all: 24805 / Num. unique obs: 2134 / CC1/2: 0.818 / Rpim(I) all: 0.253 / Rrim(I) all: 0.869 / Χ2: 1.09 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→42.08 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 900 5.51 %
Rwork0.2469 --
obs0.2485 16340 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→42.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 25 106 3170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.49
X-RAY DIFFRACTIONf_dihedral_angle_d8.057428
X-RAY DIFFRACTIONf_chiral_restr0.096495
X-RAY DIFFRACTIONf_plane_restr0.031537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.820.37041560.32422526X-RAY DIFFRACTION99
2.82-3.030.34561670.29962500X-RAY DIFFRACTION99
3.03-3.340.36471110.30772561X-RAY DIFFRACTION99
3.34-3.820.25131420.24142562X-RAY DIFFRACTION99
3.82-4.810.23911440.21522590X-RAY DIFFRACTION99
4.81-42.080.2631800.22552701X-RAY DIFFRACTION99

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