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- PDB-6l90: Crystal structure of ugt transferase enzyme -

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Basic information

Entry
Database: PDB / ID: 6l90
TitleCrystal structure of ugt transferase enzyme
ComponentsGlycosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


mogroside IE synthase / quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glucosyltransferase activity
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
Mogroside I-E synthase
Similarity search - Component
Biological speciesSiraitia grosvenorii (monk fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsLi, J. / Shan, N. / Yang, J.G. / Liu, W.D. / Sun, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Acs Catalysis / Year: 2020
Title: Efficient O-Glycosylation of Triterpenes Enabled by Protein Engineering of Plant Glycosyltransferase UGT74AC1
Authors: Li, J. / Yang, J.G. / Mu, S. / Shang, N. / Liu, C. / Zhu, Y. / Cai, Y. / Liu, P. / Lin, J. / Liu, W.D. / Sun, Y.X. / Ma, Y.
History
DepositionNov 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)51,4292
Polymers51,3331
Non-polymers961
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.832, 68.877, 143.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyltransferase / ugt transferase


Mass: 51332.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (monk fruit) / Gene: UDPG1 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: K7NBW3, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.87 % / Mosaicity: 1.041 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG8000, MgAc

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 20, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→25 Å / Num. obs: 33929 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Χ2: 1.809 / Net I/σ(I): 11.6 / Num. measured all: 261957
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.02-2.097.30.76233450.8360.3050.8221.51299.9
2.09-2.188.10.50533070.9320.1880.5391.284100
2.18-2.277.70.40533470.9420.1560.4341.497100
2.27-2.398.10.27933630.9770.1040.2981.425100
2.39-2.548.10.21633660.9860.0810.2311.609100
2.54-2.747.80.16333610.990.0630.1751.91899.9
2.74-3.028.10.10233860.9960.0380.1091.761100
3.02-3.457.80.07333980.9970.0280.0782.2100
3.45-4.357.20.05134410.9980.0210.0562.69799.6
4.35-257.10.03936150.9990.0160.0422.27899.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pq6

2pq6


Resolution: 2.02→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.335 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 1776 5.2 %RANDOM
Rwork0.2167 ---
obs0.2199 32062 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.27 Å2 / Biso mean: 40.054 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å2-0 Å2
2---1.59 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 2.02→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3577 0 5 214 3796
Biso mean--30 42.02 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133663
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173400
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.6374972
X-RAY DIFFRACTIONr_angle_other_deg1.171.5737935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5335449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50423.75176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84315650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4241515
X-RAY DIFFRACTIONr_chiral_restr0.0520.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024026
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02723
LS refinement shellResolution: 2.02→2.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 111 -
Rwork0.28 2295 -
all-2406 -
obs--97.53 %

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