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- PDB-8i0d: Sb3GT1 375S/Q377H mutant complex with UDP-Glc -

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Basic information

Entry
Database: PDB / ID: 8i0d
TitleSb3GT1 375S/Q377H mutant complex with UDP-Glc
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-GLUCOSE / Glycosyltransferase
Similarity search - Component
Biological speciesScutellaria baicalensis (Baikal skullcap)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsWang, H.T. / Wang, Z.L. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81891010/81891011 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 1.1Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.2Apr 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)50,9762
Polymers50,4101
Non-polymers5661
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area19730 Å2
Unit cell
Length a, b, c (Å)47.470, 74.520, 128.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyltransferase


Mass: 50409.512 Da / Num. of mol.: 1 / Mutation: Q376E
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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Citric acid, 0.05 M BIS-TRIS propane / pH 5.0), 16% w/v Polyethylene glycol 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: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.43→47.47 Å / Num. obs: 85370 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Net I/σ(I): 24.8
Reflection shellResolution: 1.43→1.45 Å / Num. unique obs: 4352 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1-4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→44.59 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.318 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18433 4351 5.1 %RANDOM
Rwork0.1459 ---
obs0.14785 80997 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å2-0 Å20 Å2
2---0.76 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.43→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 36 222 3730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133651
X-RAY DIFFRACTIONr_bond_other_d0.0030.0153453
X-RAY DIFFRACTIONr_angle_refined_deg1.9491.6374987
X-RAY DIFFRACTIONr_angle_other_deg1.5521.5698007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5125458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00123.148162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08515601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4591514
X-RAY DIFFRACTIONr_chiral_restr0.1050.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024039
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02789
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_it6.2612.6981796
X-RAY DIFFRACTIONr_mcbond_other6.2582.6961795
X-RAY DIFFRACTIONr_mcangle_it6.0474.0332242
X-RAY DIFFRACTIONr_mcangle_other6.0484.0362243
X-RAY DIFFRACTIONr_scbond_it6.833.1841855
X-RAY DIFFRACTIONr_scbond_other6.833.1851856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4174.5972738
X-RAY DIFFRACTIONr_long_range_B_refined6.86833.3864146
X-RAY DIFFRACTIONr_long_range_B_other6.87433.2134113
X-RAY DIFFRACTIONr_rigid_bond_restr6.8437104
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 312 -
Rwork0.239 5902 -
obs--100 %

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