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- PDB-8inp: A reversible glycosyltransferase of tectorigenin - Bc7OUGT -

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Basic information

Entry
Database: PDB / ID: 8inp
TitleA reversible glycosyltransferase of tectorigenin - Bc7OUGT
ComponentsBc7OUGT
KeywordsTRANSFERASE / glycosyltransferase / UGT / GT-B fold structure / Rossmann-like domain.
Function / homologyGlycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / beta-D-glucopyranose / URIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesIris domestica (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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 10, 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)52,2753
Polymers51,6911
Non-polymers5842
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-8 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.134, 83.395, 160.478
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-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: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
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: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.12→41.7 Å / Num. obs: 38331 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.6
Reflection shellResolution: 2.12→2.18 Å / Rmerge(I) obs: 1.528 / Num. unique obs: 3086

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Processing

Software
NameVersionClassification
PHENIXv1.19.2refinement
DIALSdata reduction
PHASERphasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→40.12 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2995 1916 5.01 %
Rwork0.2424 --
obs0.2452 38249 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 37 116 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083434
X-RAY DIFFRACTIONf_angle_d0.9814662
X-RAY DIFFRACTIONf_dihedral_angle_d7.358476
X-RAY DIFFRACTIONf_chiral_restr0.053516
X-RAY DIFFRACTIONf_plane_restr0.009596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.38431350.34992523X-RAY DIFFRACTION100
2.17-2.230.37351390.3332588X-RAY DIFFRACTION100
2.23-2.30.37811480.31682538X-RAY DIFFRACTION100
2.3-2.370.33291360.31432559X-RAY DIFFRACTION100
2.37-2.460.39281530.31092543X-RAY DIFFRACTION100
2.46-2.550.33871210.29472573X-RAY DIFFRACTION100
2.55-2.670.30851320.28442569X-RAY DIFFRACTION100
2.67-2.810.32221300.2942587X-RAY DIFFRACTION100
2.81-2.990.37671270.29912604X-RAY DIFFRACTION100
2.99-3.220.35991320.29072606X-RAY DIFFRACTION100
3.22-3.540.32771550.2642589X-RAY DIFFRACTION100
3.54-4.050.25741290.22512627X-RAY DIFFRACTION100
4.05-5.110.26881360.18822657X-RAY DIFFRACTION100
5.11-40.120.25011430.19672770X-RAY DIFFRACTION99

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