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- PDB-7w1b: Glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7w1b
TitleGlycosyltransferase
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / complex
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 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIGITOXIGENIN / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWei, H. / Feng, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Functional and Structural Dissection of a Plant Steroid 3-O-Glycosyltransferase Facilitated the Engineering Enhancement of Sugar Donor Promiscuity
Authors: Huang, W. / He, Y. / Jiang, R. / Deng, Z. / Long, F.
History
DepositionNov 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8534
Polymers53,9521
Non-polymers9013
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.351, 74.141, 63.588
Angle α, β, γ (deg.)90.000, 95.760, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Glycosyltransferase / Plant steroid glycosyltransferase UGT74AN2


Mass: 53952.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calotropis gigantea (mudar) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A385Z7H9, 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 / Comment: UDP*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-DTX / DIGITOXIGENIN / 4-(3,14-DIHYDROXY-10,13-DIMETHYL-HEXADECAHYDRO-CYCLOPENTA[A]PHENANTHREN-17-YL)-5H-FURAN-2-ONE


Mass: 374.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium chloride, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→43.16 Å / Num. obs: 26886 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 0.975 / Net I/σ(I): 12.9
Reflection shellResolution: 2.15→2.22 Å / Num. unique obs: 2333 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L8Z

6l8z


Resolution: 2.15→38.79 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 1279 4.76 %
Rwork0.1792 25563 -
obs0.1813 26842 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 60 128 3692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723651
X-RAY DIFFRACTIONf_angle_d0.85494979
X-RAY DIFFRACTIONf_chiral_restr0.0502571
X-RAY DIFFRACTIONf_plane_restr0.0056621
X-RAY DIFFRACTIONf_dihedral_angle_d8.7971507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.26521330.18322851X-RAY DIFFRACTION99.87
2.24-2.340.2631290.19692841X-RAY DIFFRACTION99.43
2.34-2.460.25821380.19662837X-RAY DIFFRACTION99.9
2.46-2.620.25051560.19252788X-RAY DIFFRACTION99.86
2.62-2.820.28351440.19792853X-RAY DIFFRACTION99.6
2.82-3.10.26751430.19472833X-RAY DIFFRACTION99.7
3.1-3.550.21321460.17962806X-RAY DIFFRACTION99.03
3.55-4.470.16881480.15592848X-RAY DIFFRACTION99.37
4.47-38.790.17351420.16612906X-RAY DIFFRACTION99.61

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