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- PDB-6inh: A glycosyltransferase with UDP and the substrate -

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Basic information

Entry
Database: PDB / ID: 6inh
TitleA glycosyltransferase with UDP and the substrate
ComponentsUDP-glycosyltransferase 76G1
KeywordsTRANSFERASE / complex
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
Chem-AQ9 / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 76G1
Similarity search - Component
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhu, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31771910 China
National Natural Science Foundation of China21534008 China
CitationJournal: Nat Commun / Year: 2019
Title: Hydrophobic recognition allows the glycosyltransferase UGT76G1 to catalyze its substrate in two orientations.
Authors: Yang, T. / Zhang, J. / Ke, D. / Yang, W. / Tang, M. / Jiang, J. / Cheng, G. / Li, J. / Cheng, W. / Wei, Y. / Li, Q. / Naismith, J.H. / Zhu, X.
History
DepositionOct 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glycosyltransferase 76G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0326
Polymers53,1581
Non-polymers1,8745
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.553, 97.553, 90.774
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-799-

HOH

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Components

#1: Protein UDP-glycosyltransferase 76G1


Mass: 53158.227 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: Chemical ChemComp-AQ9 / 1-O-[(8alpha,9beta,10alpha,13alpha)-13-(beta-D-glucopyranosyloxy)-18-oxokaur-16-en-18-yl]-beta-D-glucopyranose / Rubusoside


Mass: 642.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H50O13
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate buffer at pH 5.4 and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→84.46 Å / Num. obs: 29548 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.091 / Rrim(I) all: 0.158 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.29 / Num. unique obs: 2159 / CC1/2: 0.916 / Rpim(I) all: 0.212 / Rrim(I) all: 0.361

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQ6

2pq6


Resolution: 2.1→61.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.853 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19778 2267 5 %RANDOM
Rwork0.16706 ---
obs0.16859 29548 99.63 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.764 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.34 Å20 Å2
2---0.68 Å20 Å2
3---2.19 Å2
Refinement stepCycle: 1 / Resolution: 2.1→61.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 116 199 3922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193884
X-RAY DIFFRACTIONr_bond_other_d0.0020.023568
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9965304
X-RAY DIFFRACTIONr_angle_other_deg0.9338312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81523.898177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0715652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0971526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02796
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5162.1761833
X-RAY DIFFRACTIONr_mcbond_other2.5162.1741832
X-RAY DIFFRACTIONr_mcangle_it3.6543.2482301
X-RAY DIFFRACTIONr_mcangle_other3.6543.252302
X-RAY DIFFRACTIONr_scbond_it3.6642.7322051
X-RAY DIFFRACTIONr_scbond_other3.6632.7332052
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3813.9533002
X-RAY DIFFRACTIONr_long_range_B_refined7.28827.4534416
X-RAY DIFFRACTIONr_long_range_B_other7.28727.4644417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 123 -
Rwork0.356 3106 -
obs--96.62 %
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)
11.10840.1907-0.10662.8709-0.83651.37490.08120.01250.12960.24050.07450.3511-0.2739-0.1847-0.15570.07440.04870.03770.04090.02990.155123.836323.140525.426
22.334-2.2912.52835.64130.21094.8787-0.0705-0.2190.0810.1618-0.17020.1227-0.0047-0.56150.24070.0184-0.0002-0.01560.20130.00530.245411.146531.81748.6612
30.9420.1632-0.20393.1401-0.83181.2220.05790.05910.2054-0.03690.00440.1473-0.1891-0.1838-0.06230.09190.06130.0190.05040.03470.129426.312931.040816.9498
41.98850.51220.63742.40021.47245.4332-0.15840.56330.0541-0.74410.0413-0.0339-0.21310.27040.11710.27160.02130.04850.20280.06360.058537.950611.36-3.2632
50.6117-0.4505-0.17032.2587-0.51080.82460.09990.10910.0782-0.2426-0.1247-0.1408-0.0752-0.03460.02470.05270.02810.01110.03240.03280.090636.169417.186914.6159
62.83390.8508-0.09663.0487-1.5092.12940.03810.35690.0841-0.4370.22560.68010.3425-0.4179-0.26370.0973-0.0517-0.13720.14420.04150.259817.1248-4.220112.0001
71.88090.1575-0.11542.814-0.57321.42440.02410.2815-0.1219-0.48910.03390.29220.2841-0.1708-0.05790.1162-0.0155-0.05940.0682-0.01080.117126.8-3.274811.6211
80.8414-0.52610.40247.85750.04861.4178-0.0370.00120.130.3177-0.1099-0.1609-0.17240.10240.14690.0362-0.0194-0.02390.0120.01650.075242.546216.103328.7326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 69
2X-RAY DIFFRACTION2A70 - 78
3X-RAY DIFFRACTION3A79 - 145
4X-RAY DIFFRACTION4A146 - 197
5X-RAY DIFFRACTION5A198 - 261
6X-RAY DIFFRACTION6A262 - 316
7X-RAY DIFFRACTION7A317 - 431
8X-RAY DIFFRACTION8A432 - 460

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