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- PDB-6ini: a glycosyltransferase complex with UDP and the product -

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Basic information

Entry
Database: PDB / ID: 6ini
Titlea glycosyltransferase complex with UDP and the product
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 / Chem-AUO / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 76G1
Similarity search - Component
Biological speciesStevia rebaudiana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhu, X. / Yang, T. / Naismith, J.H.
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)55,1025
Polymers53,1581
Non-polymers1,9444
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-10 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.662, 97.662, 89.626
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-872-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 277 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AUO / (8alpha,9beta,10alpha,13alpha)-13-{[beta-D-glucopyranosyl-(1->2)-[beta-D-glucopyranosyl-(1->3)]-beta-D-glucopyranosyl]oxy}kaur-16-en-18-oic acid


Mass: 804.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H60O18
#5: 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.: 1 / Source method: obtained synthetically / Formula: C32H50O13
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
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: Jan 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→42.88 Å / Num. obs: 54657 / % possible obs: 100 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Rrim(I) all: 0.088 / Net I/σ(I): 18.9
Reflection shellResolution: 1.7→1.74 Å / Rmerge(I) obs: 1.139 / Num. unique obs: 4025 / Rpim(I) all: 0.38 / Rrim(I) all: 1.201

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQ6

2pq6


Resolution: 1.7→42.88 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.25 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19016 2725 5 %RANDOM
Rwork0.16115 ---
obs0.16259 51453 99.13 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 31.239 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.32 Å20 Å2
2---0.64 Å20 Å2
3---2.08 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 121 273 4001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173587
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.6855308
X-RAY DIFFRACTIONr_angle_other_deg1.3761.618356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84622.079202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43215655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7491526
X-RAY DIFFRACTIONr_chiral_restr0.0890.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
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_it1.5441.6171821
X-RAY DIFFRACTIONr_mcbond_other1.5421.6151820
X-RAY DIFFRACTIONr_mcangle_it2.2872.4212281
X-RAY DIFFRACTIONr_mcangle_other2.2882.4232282
X-RAY DIFFRACTIONr_scbond_it2.6641.9842062
X-RAY DIFFRACTIONr_scbond_other2.6641.9842062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0322.8653022
X-RAY DIFFRACTIONr_long_range_B_refined6.14620.5684429
X-RAY DIFFRACTIONr_long_range_B_other6.14820.5354426
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 222 -
Rwork0.238 3773 -
obs--99.33 %
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)
12.55621.075-0.66251.8487-0.18311.68610.2103-0.09980.49780.19-0.0260.2611-0.24010.1572-0.18430.1058-0.02180.08930.02680.0070.202832.2469-7.29068.7553
22.94170.8264-0.29542.2851-0.05841.16430.06870.00640.37980.03830.0470.1198-0.21180.0249-0.11570.0925-0.02580.04720.0360.03380.142439.755-5.2441.532
31.38670.5711-0.20691.4076-0.21520.7902-0.10150.34250.0188-0.27040.13940.02450.02680.0023-0.03790.0983-0.01740.020.10280.03810.091631.7708-23.7587-7.5048
43.6615-0.1026-1.14942.7677-0.31811.87610.13410.64060.7674-0.33880.20410.3918-0.2137-0.4881-0.33830.09140.04970.00440.21720.25590.39034.7151-15.582-4.7122
54.86062.46020.417111.0444-4.86625.9738-0.0045-0.068-0.1-0.52120.14560.9144-0.0493-0.6844-0.14110.11350.1059-0.01190.2280.06330.4068-3.9396-14.8651-3.0859
61.82940.4609-0.3321.2953-0.48950.9539-0.03130.23330.0996-0.10750.12010.18120.0385-0.1152-0.08880.0353-0.00070.00910.0450.04720.101317.9251-27.61040.3057
74.8306-3.7932-0.7944.04133.07065.8202-0.07680.04480.018-0.05710.00460.0711-0.24410.02930.07220.102-0.00260.01670.07740.13930.285518.1249-15.26210.9124
85.06031.5977-3.688810.7064-4.47823.77290.08130.04560.2363-0.46140.13450.23430.081-0.0627-0.21580.0664-0.0306-0.02920.02310.02860.043527.3397-12.6767-9.4709
915.00210.5160.541310.4157-0.05040.08240.2273-0.14630.01180.0694-0.19840.24940.03880.0162-0.02890.17860.04520.00170.09630.00910.076438.5148-33.53498.0428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 76
2X-RAY DIFFRACTION2A77 - 139
3X-RAY DIFFRACTION3A140 - 262
4X-RAY DIFFRACTION4A263 - 324
5X-RAY DIFFRACTION5A325 - 335
6X-RAY DIFFRACTION6A336 - 460
7X-RAY DIFFRACTION7A501
8X-RAY DIFFRACTION8A503
9X-RAY DIFFRACTION9A504

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