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Basic information

Entry
Database: PDB / ID: 9hua
TitleGlycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Complex with UDP.
ComponentsGlucosyltransferase 3
KeywordsTRANSFERASE / glycosyl transferase / GT113
Function / homologyGlucosyltransferase 3 / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / : / nucleotide binding / URIDINE-5'-DIPHOSPHATE / Glucosyltransferase 3
Function and homology information
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAsworth, G.J. / Griffiths, R. / Juge, N. / Dong, C.J. / Hemmings, A.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2025
Title: A structural basis for the strain-dependent UDP-sugar specificity of glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system.
Authors: Griffiths, R. / Pfalzgraf, H. / Latousakis, D. / Ashworth, G. / Dong, C. / Hemmings, A. / Juge, N.
History
DepositionDec 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 2.0Dec 10, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_sites / atom_type / cell / citation / citation_author / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_sheet_range / symmetry
Item: _atom_sites.fract_transf_matrix[1][3] / _cell.angle_alpha ..._atom_sites.fract_transf_matrix[1][3] / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.volume / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_number_of_molecules / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _reflns.d_resolution_low / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Atomic clashes
Details: Re-refinement of atomic model following reviewers' requests.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosyltransferase 3
B: Glucosyltransferase 3
C: Glucosyltransferase 3
D: Glucosyltransferase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,7387
Polymers161,5264
Non-polymers1,2123
Water86548
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12400 Å2
ΔGint-72 kcal/mol
Surface area49360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.406, 70.687, 140.312
Angle α, β, γ (deg.)90, 91.374, 90
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

End auth comp-ID: TYR / End label comp-ID: TYR

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRAA2 - 33422 - 354
211THRTHRBB2 - 33422 - 354
322HISHISAA0 - 33420 - 354
422HISHISCC0 - 33420 - 354
533THRTHRAA2 - 33422 - 354
633THRTHRDD2 - 33422 - 354
744THRTHRBB2 - 33422 - 354
844THRTHRCC2 - 33422 - 354
955THRTHRBB2 - 33422 - 354
1055THRTHRDD2 - 33422 - 354
1166THRTHRCC2 - 33422 - 354
1266THRTHRDD2 - 33422 - 354

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Glucosyltransferase 3


Mass: 40381.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus reuteri (bacteria) / Strain: subsp. rodentium 100-23 / Gene: gtf3, gtfC, Lreu23DRAFT_5181 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3XPQ7, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: To produce cocrystals of the UDP complex His6-tagged apo-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9, 150 mM NaCl was incubated with UDP at a final concentration of 1 mM. ...Details: To produce cocrystals of the UDP complex His6-tagged apo-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9, 150 mM NaCl was incubated with UDP at a final concentration of 1 mM. Crystals formed in 0.1 M Bis-Tris pH 7.5, 0.2 M potassium thiocyanate, 20 % (w/v) PEG 3350 after 14 days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→70.234 Å / Num. obs: 43913 / % possible obs: 99.55 % / Redundancy: 7 % / Biso Wilson estimate: 49.36 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.15
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 4322 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→70.234 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 44.485 / SU ML: 0.401 / Cross valid method: FREE R-VALUE / ESU R Free: 0.37
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2761 2166 4.935 %
Rwork0.2257 41723 -
all0.228 --
obs-43889 99.939 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70.527 Å2
Baniso -1Baniso -2Baniso -3
1-3.169 Å20 Å20.631 Å2
2---0.556 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 2.6→70.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10569 0 75 48 10692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01210947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169993
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.78514941
X-RAY DIFFRACTIONr_angle_other_deg0.6371.74722935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8251310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.836536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.176101714
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.25410553
X-RAY DIFFRACTIONr_chiral_restr0.090.21637
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212973
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022629
X-RAY DIFFRACTIONr_nbd_refined0.2290.22458
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.29565
X-RAY DIFFRACTIONr_nbtor_refined0.1910.25316
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1810.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3670.226
X-RAY DIFFRACTIONr_nbd_other0.2920.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.26
X-RAY DIFFRACTIONr_mcbond_it1.811.8165261
X-RAY DIFFRACTIONr_mcbond_other1.8091.8165261
X-RAY DIFFRACTIONr_mcangle_it2.9883.2586561
X-RAY DIFFRACTIONr_mcangle_other2.9883.2586562
X-RAY DIFFRACTIONr_scbond_it2.2162.0545686
X-RAY DIFFRACTIONr_scbond_other2.2162.0545686
X-RAY DIFFRACTIONr_scangle_it3.5973.7218379
X-RAY DIFFRACTIONr_scangle_other3.5973.7218380
X-RAY DIFFRACTIONr_lrange_it5.97218.47112391
X-RAY DIFFRACTIONr_lrange_other5.97218.47112392
X-RAY DIFFRACTIONr_ncsr_local_group_10.1250.059958
X-RAY DIFFRACTIONr_ncsr_local_group_20.1060.0511017
X-RAY DIFFRACTIONr_ncsr_local_group_30.1480.059809
X-RAY DIFFRACTIONr_ncsr_local_group_40.1220.059962
X-RAY DIFFRACTIONr_ncsr_local_group_50.1450.059378
X-RAY DIFFRACTIONr_ncsr_local_group_60.1480.059711
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.125430.05008
12BX-RAY DIFFRACTIONLocal ncs0.125430.05008
23AX-RAY DIFFRACTIONLocal ncs0.105740.05009
24CX-RAY DIFFRACTIONLocal ncs0.105740.05009
35AX-RAY DIFFRACTIONLocal ncs0.148250.05008
36DX-RAY DIFFRACTIONLocal ncs0.148250.05008
47BX-RAY DIFFRACTIONLocal ncs0.12190.05009
48CX-RAY DIFFRACTIONLocal ncs0.12190.05009
59BX-RAY DIFFRACTIONLocal ncs0.145040.05008
510DX-RAY DIFFRACTIONLocal ncs0.145040.05008
611CX-RAY DIFFRACTIONLocal ncs0.147860.05008
612DX-RAY DIFFRACTIONLocal ncs0.147860.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.6-2.6670.3722340.37629350.37531700.8870.8999.96850.362
2.667-2.740.3821810.37629660.37631530.880.87299.80970.365
2.74-2.820.3071570.30929120.30930710.9240.92899.93490.294
2.82-2.9060.321500.28628130.28829630.9280.9421000.268
2.906-3.0020.3991260.27927560.28428830.9010.94799.96530.26
3.002-3.1070.3431460.26626180.2727660.9350.95399.92770.247
3.107-3.2240.2931310.25125610.25426920.950.9611000.233
3.224-3.3550.2941020.22525230.22826260.950.97299.96190.21
3.355-3.5040.2851040.23623690.23824760.9430.95799.87880.221
3.504-3.6740.31140.22622390.2323530.9450.9641000.213
3.674-3.8730.271980.21621880.21822870.960.97199.95630.205
3.873-4.1070.281090.20920240.21221340.9510.97199.95310.201
4.107-4.3890.258870.18419620.18720510.9620.97999.90250.181
4.389-4.7390.232820.16818020.17118840.9690.9831000.17
4.739-5.1890.238860.16516430.16817300.9620.98599.94220.17
5.189-5.7980.187790.19814950.19815760.9780.98199.87310.201
5.798-6.6870.25650.22413460.22514110.9660.9731000.227
6.687-8.1720.182490.17611390.17611890.9740.98299.91590.185
8.172-11.4790.184500.1648940.1659440.9860.9881000.171
11.479-70.2340.377160.2915380.2925550.9250.95299.81980.321
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)
11.38750.8576-0.15171.9359-0.33811.49290.0834-0.0173-0.085-0.0465-0.1277-0.29430.14440.47180.04430.75660.1410.01330.57790.0840.0569-13.9247-1.6889-21.7347
22.6523-1.16011.03861.6564-0.62792.95630.12970.1867-0.2823-0.1347-0.17220.25120.2916-0.34770.04250.7825-0.06390.01380.4365-0.0260.0601-43.7918-3.9199-29.8565
32.62880.6451-1.47741.8652-0.8861.71910.16870.10450.27040.0392-0.21980.1738-0.23-0.1520.05110.79870.0708-0.00740.4296-0.02320.1109-40.804734.9414-39.7053
41.9253-1.6957-0.06894.4708-0.84441.8297-0.03010.174-0.2845-0.349-0.2292-0.40490.17050.65580.25940.7279-0.00430.09390.79450.21740.2786-11.675328.2885-48.9174
51.0308-0.3101-0.16462.62231.82532.72710.051-0.08150.31330.1653-0.072-0.4361-0.17440.47560.0210.715-0.086-0.08050.65870.11460.2566-8.183722.213-12.3362
61.05921.1041.81152.06262.12986.54590.10920.2038-0.555-0.14730.2181-0.31890.72080.0118-0.32730.74690.0534-0.01970.5636-0.14330.4557-45.81171.3432-56.8923
70.57120.1828-0.0111.33560.5343.65310.1027-0.02190.18460.207-0.1330.1689-0.2906-0.14380.03040.62940.00510.05480.39810.01280.1664-44.092629.2083-14.0728
81.2023-0.7958-0.89843.73422.78874.04240.13831.0524-0.2495-0.8753-0.2599-0.4528-0.08370.22880.12161.07910.26360.15441.4965-0.00770.3698-9.87551.9884-59.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp2 - 155
2X-RAY DIFFRACTION2ALLBp2 - 155
3X-RAY DIFFRACTION3ALLCp2 - 155
4X-RAY DIFFRACTION4ALLDp2 - 155
5X-RAY DIFFRACTION5ALLAp156 - 334
6X-RAY DIFFRACTION6ALLBp156 - 334
7X-RAY DIFFRACTION7ALLCp156 - 334
8X-RAY DIFFRACTION8ALLDp156 - 334

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