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- PDB-8ita: A reversible glycosyltransferase of tectorigenin - Bc7OUGT comple... -

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Basic information

Entry
Database: PDB / ID: 8ita
TitleA reversible glycosyltransferase of tectorigenin - Bc7OUGT complexed with UDP and tectorigenin
ComponentsBc7OUGT
KeywordsTRANSFERASE / glycosyltransferase / UGT / GT-B fold structure / Rossmann-like domain.
Function / homologyGlycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-R0U / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesIris domestica (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, Z.Y. / Lu, L. / Guan, Z.F. / Cheng, W.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100413 China
CitationJournal: Plant Biotechnol J / Year: 2023
Title: Functional characterization and structural basis of a reversible glycosyltransferase involves in plant chemical defence.
Authors: Cheng, W. / Fang, X. / Guan, Z. / Yao, Y. / Xu, Z. / Bi, Y. / Ren, K. / Li, J. / Chen, F. / Chen, X. / Ma, W. / Chu, Z. / Deng, Z. / Zhang, Z. / Lu, L.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Bc7OUGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3953
Polymers51,6911
Non-polymers7042
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-10 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.238, 83.474, 158.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Bc7OUGT


Mass: 51691.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Iris domestica (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-R0U / 3-(4-hydroxyphenyl)-6-methoxy-5,7-bis(oxidanyl)chromen-4-one / tectorigenin


Mass: 300.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12O6 / 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.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.16 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17M Lithium sulfate monohydrate, 0.085M Tris hydrochloride pH8.5, 25.5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→24.84 Å / Num. obs: 18983 / % possible obs: 82 % / Redundancy: 3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.865 / Num. unique obs: 2219

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→24.84 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 919 4.86 %
Rwork0.2185 --
obs0.2212 18922 80.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 47 49 3427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093465
X-RAY DIFFRACTIONf_angle_d1.0824705
X-RAY DIFFRACTIONf_dihedral_angle_d7.779499
X-RAY DIFFRACTIONf_chiral_restr0.051513
X-RAY DIFFRACTIONf_plane_restr0.012603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.38831060.3412670X-RAY DIFFRACTION85
2.63-2.80.36961540.32832610X-RAY DIFFRACTION85
2.8-3.010.32631310.28292645X-RAY DIFFRACTION84
3.01-3.310.351340.26152606X-RAY DIFFRACTION83
3.31-3.790.28741300.21722573X-RAY DIFFRACTION81
3.79-4.770.23681250.1862418X-RAY DIFFRACTION76
4.77-24.840.21361390.17362481X-RAY DIFFRACTION74

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