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- PDB-8i0e: Sb3GT1 complex with UDP -

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Basic information

Entry
Database: PDB / ID: 8i0e
TitleSb3GT1 complex with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / PLANT PROTEIN
Function / homology
Function and homology information


quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesScutellaria baicalensis (Baikal skullcap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, H.T. / Wang, Z.L. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81891010 China
CitationJournal: Nat Commun / Year: 2023
Title: Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants.
Authors: Wang, H.T. / Wang, Z.L. / Chen, K. / Yao, M.J. / Zhang, M. / Wang, R.S. / Zhang, J.H. / Agren, H. / Li, F.D. / Li, J. / Qiao, X. / Ye, M.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7172
Polymers50,3121
Non-polymers4041
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-7 kcal/mol
Surface area19170 Å2
Unit cell
Length a, b, c (Å)101.650, 61.280, 68.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

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Components

#1: Protein Glycosyltransferase


Mass: 50312.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scutellaria baicalensis (Baikal skullcap)
Gene: UGT78B4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A482AQV3, Transferases; Glycosyltransferases; Hexosyltransferases
#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.: 96 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium malonate pH 4.0, 20% PEG 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→45.71 Å / Num. obs: 34695 / % possible obs: 99 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 18.6
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1706 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1-4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.993 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23891 1703 4.9 %RANDOM
Rwork0.19987 ---
obs0.20183 32947 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.517 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å2-0 Å20 Å2
2---1.53 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3405 0 25 96 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153349
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.6444831
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5747752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52823.375160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7215585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0571513
X-RAY DIFFRACTIONr_chiral_restr0.0720.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023944
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02778
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2583.3551749
X-RAY DIFFRACTIONr_mcbond_other2.2583.3541748
X-RAY DIFFRACTIONr_mcangle_it3.45.022183
X-RAY DIFFRACTIONr_mcangle_other3.3995.0212184
X-RAY DIFFRACTIONr_scbond_it2.7923.7281795
X-RAY DIFFRACTIONr_scbond_other2.7923.7281794
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.475.4532645
X-RAY DIFFRACTIONr_long_range_B_refined5.81539.1013858
X-RAY DIFFRACTIONr_long_range_B_other5.80139.0383846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.947 Å
RfactorNum. reflection% reflection
Rfree0.366 92 -
Rwork0.275 2446 -
obs--99.92 %

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