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- PDB-9htx: Glycosyltransferase C from the Limosilactobacillus reuteri access... -

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Basic information

Entry
Database: PDB / ID: 9htx
TitleGlycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Apo form.
ComponentsGlucosyltransferase 3
KeywordsTRANSFERASE / glycosyl transferase / GT113
Function / homologyGlucosyltransferase 3 / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / : / nucleotide binding / Glucosyltransferase 3
Function and homology information
Biological speciesLimosilactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPfalzgraf, H.E. / Griffiths, R. / Juge, N. / 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 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 2.0Nov 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / cell / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_contact_author / pdbx_database_related / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / 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_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_sheet_range / symmetry
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_ligand_of_interest / _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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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 / _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 / _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_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.d_resolution_low / _struct_mon_prot_cis.pdbx_omega_angle / _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)161,97410
Polymers161,5264
Non-polymers4496
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-73 kcal/mol
Surface area50820 Å2
Unit cell
Length a, b, c (Å)70.439, 140.491, 145.324
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
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
111HISHISAA0 - 33320 - 353
211HISHISBB0 - 33320 - 353
322HISHISAA0 - 33420 - 354
422HISHISCC0 - 33420 - 354
533HISHISAA0 - 33320 - 353
633HISHISDD0 - 33320 - 353
744ARGARGBB-3 - 33417 - 354
844ARGARGCC-3 - 33417 - 354
955SERSERBB-1 - 33319 - 353
1055SERSERDD-1 - 33319 - 353
1166SERSERCC-1 - 33419 - 354
1266SERSERDD-1 - 33419 - 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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 apo-enzyme crystallisation screening were conducted with the purified His6-tag-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9 200 mM NaCl. ...Details: To produce cocrystals of the apo-enzyme crystallisation screening were conducted with the purified His6-tag-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9 200 mM NaCl. Crystals formed in 0.1 M Bis-Tris pH 7.5, 0.2 M potassium thiocyanate, 20% (w/v) polyethylene glycol (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→72.768 Å / Num. obs: 98062 / % possible obs: 99.63 % / Redundancy: 20 % / Biso Wilson estimate: 40.62 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 20.47
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 9711 / CC1/2: 0.781

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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→72.768 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 17.263 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2528 5101 5.204 %
Rwork0.2072 92914 -
all0.21 --
obs-98015 99.922 %
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: 70.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.597 Å2-0 Å2-0 Å2
2---3.023 Å20 Å2
3---3.62 Å2
Refinement stepCycle: LAST / Resolution: 2→72.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10810 0 26 165 11001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01211118
X-RAY DIFFRACTIONr_bond_other_d0.0030.01610227
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.78515151
X-RAY DIFFRACTIONr_angle_other_deg0.9131.74623475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.51151339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.32538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92101768
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.98710564
X-RAY DIFFRACTIONr_chiral_restr0.1310.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213226
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022670
X-RAY DIFFRACTIONr_nbd_refined0.2060.22201
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.29385
X-RAY DIFFRACTIONr_nbtor_refined0.1770.25383
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.26147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.280.229
X-RAY DIFFRACTIONr_nbd_other0.2140.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2540.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it4.6323.3795371
X-RAY DIFFRACTIONr_mcbond_other4.6323.3795371
X-RAY DIFFRACTIONr_mcangle_it6.2766.066705
X-RAY DIFFRACTIONr_mcangle_other6.2756.066706
X-RAY DIFFRACTIONr_scbond_it5.7253.7795747
X-RAY DIFFRACTIONr_scbond_other5.7253.785748
X-RAY DIFFRACTIONr_scangle_it7.9396.7848446
X-RAY DIFFRACTIONr_scangle_other7.9386.7858447
X-RAY DIFFRACTIONr_lrange_it10.37636.3212277
X-RAY DIFFRACTIONr_lrange_other10.38236.1912246
X-RAY DIFFRACTIONr_ncsr_local_group_10.1220.0510493
X-RAY DIFFRACTIONr_ncsr_local_group_20.1350.0510175
X-RAY DIFFRACTIONr_ncsr_local_group_30.1320.0510345
X-RAY DIFFRACTIONr_ncsr_local_group_40.1270.0510376
X-RAY DIFFRACTIONr_ncsr_local_group_50.1220.0510522
X-RAY DIFFRACTIONr_ncsr_local_group_60.140.0510160
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.121550.05007
12BX-RAY DIFFRACTIONLocal ncs0.121550.05007
23AX-RAY DIFFRACTIONLocal ncs0.13490.05007
24CX-RAY DIFFRACTIONLocal ncs0.13490.05007
35AX-RAY DIFFRACTIONLocal ncs0.132390.05007
36DX-RAY DIFFRACTIONLocal ncs0.132390.05007
47BX-RAY DIFFRACTIONLocal ncs0.127390.05007
48CX-RAY DIFFRACTIONLocal ncs0.127390.05007
59BX-RAY DIFFRACTIONLocal ncs0.122450.05007
510DX-RAY DIFFRACTIONLocal ncs0.122450.05007
611CX-RAY DIFFRACTIONLocal ncs0.140240.05007
612DX-RAY DIFFRACTIONLocal ncs0.140240.05007
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
2-2.0520.3713820.37467740.37471620.6440.67199.91620.367
2.052-2.1080.4773210.43466360.43669710.7230.74699.79920.439
2.108-2.1690.3353370.31764470.31867930.8970.89999.86750.295
2.169-2.2360.333820.30162150.30366100.9010.91699.80330.276
2.236-2.3090.43290.35360730.35564240.7980.80599.65750.332
2.309-2.390.2763190.22358680.22661900.9430.9699.95150.182
2.39-2.480.2373100.20356720.20459820.9560.971000.166
2.48-2.5810.2583180.19654590.19957790.9580.97499.96540.158
2.581-2.6960.2832930.21152770.21455740.9460.96899.92820.172
2.696-2.8270.2572810.19150080.19552910.9590.97899.96220.155
2.827-2.980.2532760.18748000.19150760.9620.9771000.154
2.98-3.160.2612570.18145410.18647980.9590.9791000.152
3.16-3.3780.2182240.1943000.19245240.970.9771000.165
3.378-3.6480.2712200.19739780.20141990.9510.97799.97620.177
3.648-3.9950.2532120.18436890.18739010.9620.9811000.17
3.995-4.4650.2011830.16133770.16335600.9770.9841000.151
4.465-5.1530.1971680.15629720.15831400.9760.9861000.148
5.153-6.3030.2681440.20425660.20727100.960.9781000.191
6.303-8.8810.199790.1820400.18121190.9780.9811000.182
8.881-72.7680.187650.22611980.22412630.9630.9631000.256
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.7754-0.5896-1.02551.52040.22172.6563-0.2409-0.6815-0.2420.5980.1674-0.12310.2243-0.22440.07350.29370.0924-0.04880.24390.04630.272128.7556-14.537323.6579
22.7773-1.05051.15292.1721-1.05322.4277-0.12780.32280.1478-0.2264-0.0405-0.4911-0.10430.30320.16830.0617-0.04450.07750.0639-0.0140.332435.524-4.7211-5.3955
32.7383-1.1135-1.01513.29060.35812.391-0.10710.30850.0279-0.36330.00780.42610.0781-0.36550.09930.063-0.0345-0.05610.07330.02780.3046-3.6025.0857-8.0175
43.2405-1.39130.95372.6519-1.4072.8129-0.4759-0.9370.39950.89340.42240.1759-0.33840.02740.05350.34610.20190.08270.3678-0.13290.3919-1.33712.748922.0758
53.7682.54120.75984.5741-0.06651.980.1224-0.7092-0.64610.46260.02610.05150.7436-0.5772-0.14840.54860.02580.16210.60010.19230.43883.5476-24.962625.2253
62.18410.58670.11535.80110.0030.3073-0.19750.00780.4861-0.16480.0903-0.7066-0.08450.27150.10720.1227-0.0703-0.04250.24730.04510.405929.879221.574-8.0336
71.89531.48990.19935.2190.72060.4358-0.0176-0.0176-0.1764-0.1928-0.03390.42970.1019-0.22760.05150.1348-0.0702-0.00640.15060.00390.25681.1858-21.7743-10.8745
82.48611.9297-0.14824.35150.09861.2799-0.0194-0.45720.61020.6937-0.0606-0.0795-0.70540.30820.080.74510.0833-0.24020.6781-0.18140.518923.373422.792427.6217
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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