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- PDB-6l8x: Crystal structure of Siraitia grosvenorii ugt transferase mutant2 -

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Basic information

Entry
Database: PDB / ID: 6l8x
TitleCrystal structure of Siraitia grosvenorii ugt transferase mutant2
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 (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 8, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase


Theoretical massNumber of molelcules
Total (without water)51,2211
Polymers51,2211
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20190 Å2
Unit cell
Length a, b, c (Å)50.614, 69.042, 143.991
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: 51221.477 Da / Num. of mol.: 1 / Mutation: H18A,D111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 49.92 %
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: 1.55→25 Å / Num. obs: 71652 / % possible obs: 96.4 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.032 / Rrim(I) all: 0.123 / Χ2: 1.479 / Net I/σ(I): 10 / Num. measured all: 956690
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.616.50.69864080.8670.2790.7540.54987.9
1.61-1.678.60.81769840.8490.2790.8650.57895.4
1.67-1.75110.88470580.8540.2650.9250.62495.9
1.75-1.8413.30.67970890.950.1870.7050.7496.3
1.84-1.9514.90.41971230.9860.110.4331.02296.7
1.95-2.115.60.24772080.9940.0640.2551.33197.5
2.1-2.3115.70.16172600.9940.0420.1671.68697.9
2.31-2.6515.90.12873120.9950.0340.1331.86898.4
2.65-3.3415.80.10874440.9960.0280.1112.44798.9
3.34-2515.10.09977660.9940.0260.1022.34199.2

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Processing

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

2pq6


Resolution: 1.55→24.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.547 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 3603 5 %RANDOM
Rwork0.1884 ---
obs0.1899 67899 96.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.61 Å2 / Biso mean: 31.072 Å2 / Biso min: 15.06 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2---0.71 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 1.55→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 0 345 3914
Biso mean---41.94 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133654
X-RAY DIFFRACTIONr_bond_other_d00.0173400
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.6374960
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5727933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8445449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9623.736174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89815648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5171515
X-RAY DIFFRACTIONr_chiral_restr0.0770.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.024016
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02721
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 230 -
Rwork0.251 4420 -
all-4650 -
obs--86.24 %

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