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- PDB-8inh: ZjOGT3, flavonoid 7,4'-di-O-glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 8inh
TitleZjOGT3, flavonoid 7,4'-di-O-glycosyltransferase
ComponentsGlycosyltransferase
KeywordsPLANT PROTEIN / glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesZiziphus jujuba var. spinosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, Z.L. / Wang, H.D. / Li, F.D. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81725023 China
CitationJournal: Chem Sci / Year: 2023
Title: Functional characterization, structural basis, and regio-selectivity control of a promiscuous flavonoid 7,4'-di- O -glycosyltransferase from Ziziphus jujuba var. spinosa.
Authors: Wang, Z.L. / Wei, W. / Wang, H.D. / Zhou, J.J. / Wang, H.T. / Chen, K. / Wang, R.S. / Li, F.D. / Qiao, X. / Zhou, H. / Liang, Y. / Ye, M.
History
DepositionMar 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycosyltransferase
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,0374
Polymers107,2292
Non-polymers8082
Water181
1
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0192
Polymers53,6141
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area19780 Å2
MethodPISA
2
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0192
Polymers53,6141
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-8 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.730, 84.810, 103.630
Angle α, β, γ (deg.)90.00, 93.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosyltransferase


Mass: 53614.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ziziphus jujuba var. spinosa (plant) / Gene: FEM48_Zijuj09G0128800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A978UT44
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / 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.: 1 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium acetate trihydrate, 26% w/v PEG 4000, 10 mM Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→51.73 Å / Num. obs: 35988 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.77 Å2 / CC1/2: 0.984 / Net I/σ(I): 5.4
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 35988 / CC1/2: 0.984

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→51.73 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1737 4.83 %
Rwork0.2398 --
obs0.2415 35988 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→51.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 50 1 7211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027402
X-RAY DIFFRACTIONf_angle_d0.48110064
X-RAY DIFFRACTIONf_dihedral_angle_d4.2960
X-RAY DIFFRACTIONf_chiral_restr0.0421104
X-RAY DIFFRACTIONf_plane_restr0.0041294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.39021590.35512856X-RAY DIFFRACTION98
2.57-2.660.36141280.32782822X-RAY DIFFRACTION98
2.66-2.750.34771620.31882822X-RAY DIFFRACTION97
2.75-2.860.34441280.30962900X-RAY DIFFRACTION98
2.86-2.990.3691670.29842849X-RAY DIFFRACTION98
2.99-3.150.27991270.27122885X-RAY DIFFRACTION98
3.15-3.350.31781600.25642875X-RAY DIFFRACTION98
3.35-3.610.27721370.25352852X-RAY DIFFRACTION97
3.61-3.970.24891540.22192837X-RAY DIFFRACTION97
3.97-4.540.24151310.19112891X-RAY DIFFRACTION97
4.54-5.720.20471480.19832811X-RAY DIFFRACTION95
5.72-51.730.23381360.18632851X-RAY DIFFRACTION94

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