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- PDB-7w0k: plant glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7w0k
Titleplant glycosyltransferase
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / UGT74AN2 Complex with UDP
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
URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6335
Polymers53,9521
Non-polymers6804
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-11 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.462, 74.038, 61.815
Angle α, β, γ (deg.)90.000, 114.400, 90.000
Int Tables number4
Space group name H-MP1211

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.1 Å3/Da / Density % sol: 41.53 %
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: 2.04→48.44 Å / Num. obs: 28193 / % possible obs: 97.4 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.177 / Net I/σ(I): 8
Reflection shellResolution: 2.04→2.1 Å / Num. unique obs: 2165 / CC1/2: 0.791

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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: 2.04→48.44 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 1395 4.95 %
Rwork0.1932 26770 -
obs0.1956 28165 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.93 Å2 / Biso mean: 28.6068 Å2 / Biso min: 13.15 Å2
Refinement stepCycle: final / Resolution: 2.04→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 43 37 3629
Biso mean--26.18 24.23 -
Num. residues----457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.110.30621510.23552634278599
2.11-2.20.32841580.21712652281099
2.2-2.30.26791430.21472682282599
2.3-2.420.26971360.21262640277699
2.42-2.570.25531230.20712695281898
2.57-2.770.28071560.20762668282499
2.77-3.050.26171570.20392682283999
3.05-3.490.18621190.19412663278298
3.49-4.390.23121630.16492682284599
4.39-48.440.1994890.17592772286198
Refinement TLS params.Method: refined / Origin x: -10.699 Å / Origin y: 6.5865 Å / Origin z: -6.7084 Å
111213212223313233
T0.1512 Å2-0.0189 Å2-0.0026 Å2-0.1493 Å2-0.0086 Å2--0.1709 Å2
L0.2678 °2-0.1352 °2-0.2569 °2-0.2021 °20.2076 °2--0.7881 °2
S-0.028 Å °0.0292 Å °-0.0285 Å °0.0031 Å °-0.0235 Å °0.002 Å °0.0557 Å °-0.0293 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 477
2X-RAY DIFFRACTION1allA504 - 507
3X-RAY DIFFRACTION1allS1 - 245

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