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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 / protein glycosylation / 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: 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 20, 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


Theoretical massNumber of molelcules
Total (without water)161,5264
Polymers161,5264
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-54 kcal/mol
Surface area51220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.439, 140.491, 145.324
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

#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
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→72.66 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
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→72.66 Å / SU ML: 0.2907 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 5089 5.21 %
Rwork0.2284 92618 -
obs0.2304 97707 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70 Å2
Refinement stepCycle: LAST / Resolution: 2→72.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10872 0 0 207 11079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008611179
X-RAY DIFFRACTIONf_angle_d0.967115237
X-RAY DIFFRACTIONf_chiral_restr0.05821660
X-RAY DIFFRACTIONf_plane_restr0.00841974
X-RAY DIFFRACTIONf_dihedral_angle_d6.47691457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.44651870.41763045X-RAY DIFFRACTION99.75
2.02-2.050.37011680.37013027X-RAY DIFFRACTION99.66
2.05-2.070.56551440.48623063X-RAY DIFFRACTION98.31
2.07-2.10.46021480.38573043X-RAY DIFFRACTION99.47
2.1-2.130.38721430.3473085X-RAY DIFFRACTION99.72
2.13-2.150.32681700.32363039X-RAY DIFFRACTION99.75
2.15-2.190.38181730.31763040X-RAY DIFFRACTION99.54
2.19-2.220.3371860.31833047X-RAY DIFFRACTION99.63
2.22-2.250.47881770.39562976X-RAY DIFFRACTION97.83
2.25-2.290.37071630.33743039X-RAY DIFFRACTION99.41
2.29-2.330.35051540.28273102X-RAY DIFFRACTION99.79
2.33-2.370.31371690.25643054X-RAY DIFFRACTION99.69
2.37-2.420.28061790.24753077X-RAY DIFFRACTION99.91
2.42-2.470.28651670.22493073X-RAY DIFFRACTION99.94
2.47-2.520.30281650.22393087X-RAY DIFFRACTION99.72
2.52-2.580.27011860.22863018X-RAY DIFFRACTION99.78
2.58-2.640.27671810.23093086X-RAY DIFFRACTION99.79
2.64-2.710.31371560.25833085X-RAY DIFFRACTION99.85
2.71-2.790.28711760.24763093X-RAY DIFFRACTION99.91
2.79-2.880.31461810.25693075X-RAY DIFFRACTION99.85
2.88-2.990.31311780.24693072X-RAY DIFFRACTION99.94
2.99-3.110.26511560.23193117X-RAY DIFFRACTION99.94
3.11-3.250.23641850.21763094X-RAY DIFFRACTION99.97
3.25-3.420.24441710.21963115X-RAY DIFFRACTION99.94
3.42-3.630.26021670.21693112X-RAY DIFFRACTION99.97
3.63-3.910.25571840.19973140X-RAY DIFFRACTION100
3.91-4.310.20761610.18373124X-RAY DIFFRACTION100
4.31-4.930.22631790.17633173X-RAY DIFFRACTION99.94
4.93-6.210.23941830.20743189X-RAY DIFFRACTION100
6.21-100.191520.193328X-RAY DIFFRACTION98.36
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)
13.34593067278-0.2537275306070.3789756354731.55633884858-0.04315707955731.59331252038-0.283778527786-0.822893389136-0.4993834239320.4534421142150.3193482159810.01934018093320.301314852073-0.383633124346-0.00543713319990.5722030194770.1193599212380.08785319526730.5927732485420.2033519307850.47319046547215.3955710138-19.999803420224.3607109303
22.32859055181-1.059851328340.4893144885142.82128179875-0.4834435877220.909283825306-0.181790894570.2051024824580.50885716432-0.0532527538023-0.010015034503-0.731554350897-0.1284081584250.1945499136630.1359101670240.302529709085-0.05248573204750.02625576478350.3437524805560.002436655970660.61785539345132.33772472918.95722482168-6.62551702935
31.35489346271-0.637243698929-0.09522971253623.396991273170.3362529340820.883793534094-0.07044369184740.118507649064-0.127467902689-0.2542091159510.02282726257680.6351978299930.0825467940649-0.1883200847580.02393243021390.291614114806-0.0606611820656-0.01972992543830.3365571710230.03887490506910.565308771131-1.10755663787-9.04695171965-9.41779916565
42.00233519192-0.1169058204150.4226800469051.66647176103-0.6883515773511.48259052887-0.492434084028-0.7122069012650.5206012792970.9061217427590.2990715464870.000421127446833-0.5100515397950.07035153070820.1149715808190.796869255120.233618493195-0.1346454012380.661823915248-0.2550797458360.56290256631411.744306921117.951934739424.8457082692
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)AA-1 - 3341 - 336
22(chain 'B' and resid -3 through 334)BB-3 - 3341 - 338
33(chain 'C' and resid -4 through 334)CC-4 - 3341 - 339
44(chain 'D' and resid -1 through 334)DD-1 - 3341 - 336

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