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- PDB-9hu9: Glycosyltransferase C from the Limosilactobacillus reuteri access... -

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Basic information

Entry
Database: PDB / ID: 9hu9
TitleGlycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Complex with UDP-GlcNAc.
ComponentsGlucosyltransferase 3
KeywordsTRANSFERASE / glycosyl transferase / GT113
Function / homologyGlucosyltransferase 3 / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / : / nucleotide binding / CITRIC ACID / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / URIDINE-5'-DIPHOSPHATE / Glucosyltransferase 3
Function and homology information
Biological speciesLimosilactobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPfalzgraf, H.E. / Griffiths, R. / Juge, N. / Hemmings, A.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
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.E. / Latousakis, D. / Dong, C.J. / Hemmings, A.M. / Juge, N.
History
DepositionDec 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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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)156,44112
Polymers153,9694
Non-polymers2,4728
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-46 kcal/mol
Surface area49040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.639, 121.392, 174.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucosyltransferase 3


Mass: 38492.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limosilactobacillus (bacteria) / Gene: gtf3, gtfC, Lreu23DRAFT_5181 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B3XPQ7, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 6 types, 204 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: ammonium hydrogen citrate, PEG 3350

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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: 2.4→60.7 Å / Num. obs: 64276 / % possible obs: 99.68 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.52 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.099 / Net I/σ(I): 5.62
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 0.58 / Num. unique obs: 6327 / CC1/2: 0.516 / Rpim(I) all: 0.9018

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→60.7 Å / SU ML: 0.3068 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 3204 5 %
Rwork0.1814 60874 -
obs0.1836 64078 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10848 0 158 196 11202
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008611303
X-RAY DIFFRACTIONf_angle_d0.978315420
X-RAY DIFFRACTIONf_chiral_restr0.05811674
X-RAY DIFFRACTIONf_plane_restr0.00741975
X-RAY DIFFRACTIONf_dihedral_angle_d9.03251479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.33121170.28472562X-RAY DIFFRACTION98.2
2.44-2.470.34391250.29282594X-RAY DIFFRACTION97.21
2.47-2.510.32451410.27972559X-RAY DIFFRACTION99.67
2.51-2.560.30041350.26762636X-RAY DIFFRACTION99.71
2.56-2.60.29191340.24722613X-RAY DIFFRACTION99.85
2.6-2.650.30721500.2382640X-RAY DIFFRACTION99.82
2.65-2.710.30191240.23742602X-RAY DIFFRACTION99.85
2.71-2.770.26421560.2292619X-RAY DIFFRACTION99.78
2.77-2.830.28081440.23622631X-RAY DIFFRACTION99.86
2.83-2.90.28071370.23342595X-RAY DIFFRACTION99.93
2.9-2.980.28861340.23252648X-RAY DIFFRACTION99.89
2.98-3.070.28241240.21322661X-RAY DIFFRACTION99.89
3.07-3.170.24461520.21372629X-RAY DIFFRACTION100
3.17-3.280.27621410.19432627X-RAY DIFFRACTION99.93
3.28-3.410.22231450.18762633X-RAY DIFFRACTION99.93
3.41-3.570.23941610.18272625X-RAY DIFFRACTION99.86
3.57-3.760.24741470.16612648X-RAY DIFFRACTION99.89
3.76-3.990.1881250.1542680X-RAY DIFFRACTION99.93
3.99-4.30.17791370.13662673X-RAY DIFFRACTION99.96
4.3-4.730.16871550.13162681X-RAY DIFFRACTION100
4.73-5.420.15661370.13972705X-RAY DIFFRACTION100
5.42-6.820.23371450.17642740X-RAY DIFFRACTION100
6.82-100.17761380.152873X-RAY DIFFRACTION100
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)
11.361087578790.3621756740430.03244273210521.901530210760.8238822457781.584504099380.09948442795220.232068878461-0.116338858334-0.18612156297-0.0270616824247-0.0851956697346-0.182432928606-0.0440487495536-0.06097300647620.2932688269810.03098071471240.009011832725560.326232046970.02769978583720.26851013315635.471998014916.86793095095.78974176137
20.687333116837-0.126048615563-0.05169386715531.66344284674-0.6011735951441.59529485546-0.0455636935767-0.156655231901-0.06648342080690.1325737203380.02637325221610.0897023605336-0.0366653312697-0.07791590525090.02626683770190.284030061823-0.00787021678894-0.01077547223780.315800543539-0.003700541265080.31259941273516.848167188129.261919492546.1419023267
31.02225365018-0.3665526192170.4163834602141.1293020915-1.016405846761.61118339090.06800827559220.0398078437278-0.119748798255-0.0713940923603-0.0417862013853-0.05083125467790.119941974628-0.0113472509942-0.02625259468760.298785696178-0.01487019249760.01884035035210.29675227515-0.01936972742320.3781258817370.9519177410944.9738156044620.9953936839
41.237360565970.2233403137460.5189261300291.807293020430.5853239974531.137650363630.00705998952352-0.0564353983435-0.08970009399020.1337781779540.0334892107761-0.0001750141601650.03788849159660.0958013352747-0.04684197018570.3248167980790.02213227627260.03302894075450.346922296090.04162974538620.34501321329943.01078739180.70715388039539.7030760806
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 334)AA1 - 3341 - 334
22(chain 'B' and resid 0 through 334)BE0 - 3341 - 335
33(chain 'C' and resid -1 through 334)CH-1 - 3341 - 336
44(chain 'D' and resid 0 through 334)DL0 - 3341 - 335

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