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- PDB-6o86: Crystal Structure of SeMet UDP-dependent glucosyltransferases (UG... -

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Basic information

Entry
Database: PDB / ID: 6o86
TitleCrystal Structure of SeMet UDP-dependent glucosyltransferases (UGT) from Stevia rebaudiana in complex with UDP
ComponentsUDP-glycosyltransferase 76G1
KeywordsTRANSFERASE / plant biochemistry
Function / homology
Function and homology information


UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
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 / UDP-glycosyltransferase 76G1
Similarity search - Component
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Molecular basis for branched steviol glucoside biosynthesis.
Authors: Lee, S.G. / Salomon, E. / Yu, O. / Jez, J.M.
History
DepositionMar 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: UDP-glycosyltransferase 76G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4912
Polymers52,0871
Non-polymers4041
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.982, 97.982, 90.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-848-

HOH

21A-881-

HOH

31A-899-

HOH

41A-983-

HOH

51A-984-

HOH

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Components

#1: Protein UDP-glycosyltransferase 76G1


Mass: 52087.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stevia rebaudiana (plant) / Gene: UGT76G1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6VAB4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% (w/v) PEG-4000, 20% 2-propanol (v/v), 100 mM sodium citrate tribasic dihydrate buffer pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.799→38.5 Å / Num. obs: 47033 / % possible obs: 99.6 % / Redundancy: 6.8 % / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 2332

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PHASERphasing
Cootmodel building
HKL-3000data collection
RefinementMethod to determine structure: SAD / Resolution: 1.799→38.451 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.72
RfactorNum. reflection% reflection
Rfree0.1957 2335 5.08 %
Rwork0.1732 --
obs0.1743 45957 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→38.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 25 387 3959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043661
X-RAY DIFFRACTIONf_angle_d0.7384970
X-RAY DIFFRACTIONf_dihedral_angle_d14.1482186
X-RAY DIFFRACTIONf_chiral_restr0.048545
X-RAY DIFFRACTIONf_plane_restr0.005636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.83570.27271250.23852258X-RAY DIFFRACTION87
1.8357-1.87560.23171210.21222373X-RAY DIFFRACTION91
1.8756-1.91920.25051360.20052414X-RAY DIFFRACTION92
1.9192-1.96720.22921320.18722476X-RAY DIFFRACTION95
1.9672-2.02040.21261250.18912554X-RAY DIFFRACTION98
2.0204-2.07990.21561370.17732578X-RAY DIFFRACTION99
2.0799-2.1470.17811380.1662585X-RAY DIFFRACTION99
2.147-2.22370.17721370.16582622X-RAY DIFFRACTION99
2.2237-2.31270.19311440.16732589X-RAY DIFFRACTION100
2.3127-2.4180.19141510.1682590X-RAY DIFFRACTION100
2.418-2.54540.21621320.17292644X-RAY DIFFRACTION100
2.5454-2.70490.20511230.1732648X-RAY DIFFRACTION100
2.7049-2.91370.21071470.17492623X-RAY DIFFRACTION99
2.9137-3.20670.1891380.17172642X-RAY DIFFRACTION100
3.2067-3.67050.18911780.16212615X-RAY DIFFRACTION100
3.6705-4.62310.16671390.15322664X-RAY DIFFRACTION99
4.6231-38.45930.1871320.18262747X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.33410.63120.23451.82350.93281.23630.0494-0.0393-0.15420.03820.1177-0.39040.11610.35620.04720.06660.0206-0.06420.219-0.05240.162612.03233.013924.9627
21.2210.4264-0.29490.82860.19430.31020.0632-0.59990.17990.4134-0.09370.0792-0.00730.22690.06680.2339-0.0194-0.01740.3624-0.12050.1505-2.416541.195141.3038
31.86250.85880.35072.13230.30190.97690.0796-0.3601-0.05820.2352-0.0503-0.05620.1415-0.0860.00980.06760.0182-0.03170.1261-0.00250.0357-13.257424.752130.7597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 458 )

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