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- PDB-7bv3: Crystal structure of a ugt transferase from Siraitia grosvenorii ... -

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Basic information

Entry
Database: PDB / ID: 7bv3
TitleCrystal structure of a ugt transferase from Siraitia grosvenorii in complex with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / prenyltransferase
Function / homologyUDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / chloroplast / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLi, J. / Shan, N. / Yang, J.G. / Liu, W.D. / Sun, Y.X.
CitationJournal: Green Synth Catal / Year: 2021
Title: Near-perfect control of the regioselective glucosylation enabled by rational design of glycosyltransferases
Authors: Li, J. / Qu, G. / Shang, N. / Chen, P. / Men, Y. / Liu, W.D. / Mei, Z. / Sun, Y.X. / Sun, Z.
History
DepositionApr 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4204
Polymers105,6112
Non-polymers8082
Water11,818656
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-15 kcal/mol
Surface area39000 Å2
Unit cell
Length a, b, c (Å)197.520, 63.710, 93.800
Angle α, β, γ (deg.)90.000, 101.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-889-

HOH

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Components

#1: Protein Glycosyltransferase / / ugt transferase


Mass: 52805.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Gene: UGT74AC2 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A346A6C4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 2.74 Å3/Da / Density % sol: 55.05 % / Mosaicity: 0.243 °
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: Dec 5, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. obs: 98386 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Χ2: 0.711 / Net I/σ(I): 8.8 / Num. measured all: 651819
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.926.20.72898100.8640.3170.7960.48499.9
1.92-1.996.60.48997700.9290.2040.5310.51599.9
1.99-2.086.70.32297670.970.1330.3490.508100
2.08-2.196.60.22497740.9830.0940.2430.533100
2.19-2.336.40.15398130.9910.0650.1670.604100
2.33-2.516.90.1198360.9950.0450.1190.624100
2.51-2.766.70.07998320.9970.0330.0860.8100
2.76-3.166.80.05298420.9980.0220.0570.89999.9
3.16-3.986.70.03998930.9990.0170.0431.276100
3.98-256.50.032100490.9990.0140.0350.84299.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ACW

2acw


Resolution: 1.85→24.22 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1957 4900 5.02 %
Rwork0.1736 92683 -
obs0.1747 97583 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.37 Å2 / Biso mean: 38.3874 Å2 / Biso min: 11.94 Å2
Refinement stepCycle: final / Resolution: 1.85→24.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6931 0 50 656 7637
Biso mean--25.87 42.02 -
Num. residues----896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Num. reflection Rfree: 490 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.920.25310.231491939683
1.92-1.990.24310.207592709760
1.99-2.080.23620.198191839673
2.08-2.190.21080.188392079697
2.19-2.330.22460.185392389728
2.33-2.510.19840.179292519741
2.51-2.760.21390.178792819771
2.76-3.160.19940.177692659755
3.16-3.980.1840.165793229812
3.98-24.220.16290.152994739963

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