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- PDB-7w09: UGT74AN2, Plant Steroid Glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7w09
TitleUGT74AN2, Plant Steroid Glycosyltransferase
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Apo / UGT74AN2 / Glycosyltransferase
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
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWei, H. / Feng, L.
Funding support China, 3items
OrganizationGrant numberCountry
Other government2018YFA0900400
Other government2021YFA0909500
Other government2042019kf0185 China
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 18, 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


Theoretical massNumber of molelcules
Total (without water)53,9521
Polymers53,9521
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.413, 75.446, 61.766
Angle α, β, γ (deg.)90.000, 113.839, 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 BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: A0A385Z7H9, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium chloride, MES (pH 6.5)

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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: 1.95→49.77 Å / Num. obs: 32926 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 24.17 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.067 / Rrim(I) all: 0.126 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2268 / CC1/2: 0.866 / % possible all: 97.4

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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: 1.95→30.4 Å / SU ML: 0.2279 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.6729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 1583 4.81 %
Rwork0.2017 31310 -
obs0.2033 32893 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 0 25 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793445
X-RAY DIFFRACTIONf_angle_d0.89614687
X-RAY DIFFRACTIONf_chiral_restr0.0566543
X-RAY DIFFRACTIONf_plane_restr0.0061591
X-RAY DIFFRACTIONf_dihedral_angle_d5.8925457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.27691350.24152789X-RAY DIFFRACTION97.4
2.01-2.090.27481390.21512806X-RAY DIFFRACTION98.1
2.09-2.170.24841500.21662875X-RAY DIFFRACTION99.51
2.17-2.270.2741470.2182854X-RAY DIFFRACTION99.14
2.27-2.390.2591370.21972840X-RAY DIFFRACTION99
2.39-2.540.28741470.21942799X-RAY DIFFRACTION97.84
2.54-2.730.22841360.22472896X-RAY DIFFRACTION99.57
2.73-3.010.23141390.21612857X-RAY DIFFRACTION99.11
3.01-3.440.24051320.21242842X-RAY DIFFRACTION98.02
3.44-4.330.22531760.17082846X-RAY DIFFRACTION99.38
4.34-30.40.19491450.17812906X-RAY DIFFRACTION98.07
Refinement TLS params.Method: refined / Origin x: -10.6804716418 Å / Origin y: 7.79397863673 Å / Origin z: -6.8032148354 Å
111213212223313233
T0.121261905815 Å2-0.0144354067956 Å2-0.000879031138126 Å2-0.118215288556 Å2-0.00485745245584 Å2--0.13540740738 Å2
L0.190204127103 °2-0.150372598222 °2-0.131471296159 °2-0.144864518046 °20.208095050566 °2--0.59275150008 °2
S0.00135674220492 Å °0.0361085977938 Å °-0.0245184065951 Å °-0.00547381052123 Å °-0.0276962174285 Å °0.0103658403056 Å °0.0141081128197 Å °-0.057864677615 Å °-0.000171020196369 Å °
Refinement TLS groupSelection details: all

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