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- PDB-9ksm: Complex structure of CaApiGT/UDP -

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Basic information

Entry
Database: PDB / ID: 9ksm
TitleComplex structure of CaApiGT/UDP
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: 1.74 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9592
Polymers51,5541
Non-polymers4041
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-10 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.070, 119.312, 47.677
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: 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.: 398 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
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: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 26, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.74→66.49 Å / Num. obs: 47528 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 8
Reflection shellResolution: 1.74→1.84 Å / Num. unique obs: 6848 / CC1/2: 0.481

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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: 1.74→44.27 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 2260 4.82 %
Rwork0.1943 --
obs0.1959 46904 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3600 0 25 398 4023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.987
X-RAY DIFFRACTIONf_dihedral_angle_d7.223495
X-RAY DIFFRACTIONf_chiral_restr0.061563
X-RAY DIFFRACTIONf_plane_restr0.009640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.37421190.30152500X-RAY DIFFRACTION88
1.78-1.820.36181190.28962622X-RAY DIFFRACTION95
1.82-1.870.28981530.26042745X-RAY DIFFRACTION99
1.87-1.920.29561220.25462806X-RAY DIFFRACTION100
1.92-1.970.30711410.23412758X-RAY DIFFRACTION100
1.97-2.040.2681330.21492795X-RAY DIFFRACTION100
2.04-2.110.24991360.19972817X-RAY DIFFRACTION100
2.11-2.20.21381410.19382760X-RAY DIFFRACTION100
2.2-2.30.25061590.19732831X-RAY DIFFRACTION100
2.3-2.420.2541360.19622800X-RAY DIFFRACTION100
2.42-2.570.24871490.19752813X-RAY DIFFRACTION100
2.57-2.770.24341420.20422836X-RAY DIFFRACTION100
2.77-3.040.24311410.18942821X-RAY DIFFRACTION100
3.05-3.480.19721470.182861X-RAY DIFFRACTION100
3.49-4.390.17531370.14862905X-RAY DIFFRACTION100
4.39-44.270.18361850.17412974X-RAY DIFFRACTION99

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