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- PDB-8w53: Crystal structure of LbUGT in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 8w53
TitleCrystal structure of LbUGT in complex with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Lycibarbarspermidines / Biosynthesis / Glycosyltransferase
Function / homology: / UDP-glycosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesLycium barbarum (goji berry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42816165393 Å
AuthorsHu, D. / Wang, G.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Functional and structural dissection of glycosyltransferases underlying the glycodiversity of wolfberry-derived bioactive ingredients lycibarbarspermidines.
Authors: Li, S.Y. / Wang, G.Q. / Long, L. / Gao, J.L. / Zhou, Z.Q. / Wang, Y.H. / Lv, J.M. / Chen, G.D. / Hu, D. / Abe, I. / Gao, H.
History
DepositionAug 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glycosyltransferase
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1805
Polymers109,2792
Non-polymers9003
Water81145
1
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0442
Polymers54,6401
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-10 kcal/mol
Surface area21120 Å2
MethodPISA
2
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1363
Polymers54,6401
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-9 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.442, 80.841, 180.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Glycosyltransferase


Mass: 54639.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycium barbarum (goji berry) / Gene: UGT71A14 / Production host: Escherichia coli (E. coli)
References: UniProt: B6EWZ1, Transferases; Glycosyltransferases; Hexosyltransferases
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 292.2 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis Tris propane, 200 mM Na fluoride and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.428→31.03 Å / Num. obs: 40772 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 52.3910339953 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.6
Reflection shellResolution: 2.428→2.49 Å / Redundancy: 13.3 % / Num. unique obs: 2963 / CC1/2: 0.617 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42816165393→31.0197729226 Å / SU ML: 0.365966669923 / Cross valid method: FREE R-VALUE / σ(F): 1.46908652227 / Phase error: 29.7487652113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265892277345 2000 4.91231517414 %
Rwork0.219232449049 38714 -
obs0.221550163313 40714 99.8259163908 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.9338292559 Å2
Refinement stepCycle: LAST / Resolution: 2.42816165393→31.0197729226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7502 0 56 45 7603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003376999413757722
X-RAY DIFFRACTIONf_angle_d0.67013176224510453
X-RAY DIFFRACTIONf_chiral_restr0.04302307942531168
X-RAY DIFFRACTIONf_plane_restr0.003571262348291337
X-RAY DIFFRACTIONf_dihedral_angle_d2.752201771635621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4282-2.48890.4466565462921370.3647000605552656X-RAY DIFFRACTION97.8626489138
2.4889-2.55610.3562729677451410.3304119240452718X-RAY DIFFRACTION100
2.5561-2.63130.34049496911410.3179861720032749X-RAY DIFFRACTION100
2.6313-2.71620.3765435366871410.2952558046962734X-RAY DIFFRACTION99.9652294854
2.7162-2.81320.3142756105051420.28230831672723X-RAY DIFFRACTION100
2.8132-2.92580.2893818241611410.2738000789272736X-RAY DIFFRACTION99.9652536484
2.9258-3.05880.3356260356891420.2666742900422740X-RAY DIFFRACTION100
3.0588-3.21990.3055173271251420.2643408799612758X-RAY DIFFRACTION99.9310820124
3.2199-3.42140.3282954239881420.2563021650792754X-RAY DIFFRACTION100
3.4214-3.68520.2822253917091430.2270317603382773X-RAY DIFFRACTION100
3.6852-4.05530.2636127261211440.1957415545352790X-RAY DIFFRACTION100
4.0553-4.64050.2097957527421440.171315016792776X-RAY DIFFRACTION99.9657651489
4.6405-5.84010.2422715301611460.1841150772552839X-RAY DIFFRACTION99.9665103818
5.8401-31.0190.1951111631151540.1742678332142968X-RAY DIFFRACTION99.8720409469

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