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

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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: 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)162,7387
Polymers161,5264
Non-polymers1,2123
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.406, 70.687, 140.312
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 54 / 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→70.14 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
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→70.14 Å / SU ML: 0.4547 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.2366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3079 2153 4.92 %
Rwork0.2298 41566 -
obs0.2334 43719 99.56 %
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: 2.6→70.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10628 0 75 54 10757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008311000
X-RAY DIFFRACTIONf_angle_d1.102715013
X-RAY DIFFRACTIONf_chiral_restr0.06061639
X-RAY DIFFRACTIONf_plane_restr0.00761932
X-RAY DIFFRACTIONf_dihedral_angle_d18.4353871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.43352100.37292648X-RAY DIFFRACTION99.55
2.66-2.730.44031740.38592705X-RAY DIFFRACTION98.9
2.73-2.80.4321540.33962736X-RAY DIFFRACTION99.14
2.8-2.880.40521380.31632758X-RAY DIFFRACTION99.42
2.88-2.980.39991320.30452737X-RAY DIFFRACTION99.27
2.98-3.080.41891430.28592761X-RAY DIFFRACTION99.62
3.08-3.210.37241450.28162751X-RAY DIFFRACTION99.48
3.21-3.350.32081180.26162800X-RAY DIFFRACTION99.49
3.35-3.530.33811150.25992772X-RAY DIFFRACTION99.52
3.53-3.750.31331540.22962775X-RAY DIFFRACTION99.8
3.75-4.040.27911370.20132784X-RAY DIFFRACTION99.83
4.04-4.450.27631170.18072816X-RAY DIFFRACTION99.86
4.45-5.090.25531390.17662815X-RAY DIFFRACTION99.9
5.09-6.410.22881420.21082813X-RAY DIFFRACTION99.9
6.41-100.23591350.17992895X-RAY DIFFRACTION99.64
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)
11.058395206790.2220270071570.08299487936422.371908290630.03997449032931.310258181720.0383150343576-0.05433454114020.09982792724390.193473616385-0.174982670897-0.2070423695850.1185825190890.4514163648990.1332782376530.6083303856150.0423765196807-0.02816384784080.4842788131820.0977597263860.343431278675-10.986889459911.0042790287-16.7064995972
20.105306720173-0.0764353743202-0.01441590634020.05544430528750.008846114353790.00256053097630.08381241715250.0244527223693-0.01548579461060.008397565387390.0471967478553-0.00486087022834-0.01126419880110.0310455395408-0.0002583952275190.553816302523-0.134244999756-0.07366013481210.4979165328380.1503530611850.783232587501-14.674205884614.8730505929-10.4135856942
31.10994725228-0.2692916415010.7406341756660.932100254559-0.3140916243592.343662091910.1422937824050.290232816981-0.310454479738-0.402791808294-0.1371560709460.1066381180510.627306387296-0.0450929627611-0.01886119285580.9228660796110.00720255109141-0.006406478252570.420819738535-0.09133475699570.392544837512-44.9254631225-1.36676474093-44.4062185937
40.2955159361320.0394592812925-0.1515034535660.012589754385-0.01964448400380.07779294481360.0140662063798-0.00488560872822-0.01241695796330.01631298859-0.005472002527570.1214362082460.0155978790875-0.03502933507680.000920827690931.046272931020.07342889004720.03668028761991.01748174242-0.2144882201641.17536165039-41.1866467581-5.98847362363-50.6227276758
50.7963814536110.265798592045-0.1641142515531.55265497183-0.4840739924582.061477656930.08781744914650.01266436698140.1827486159410.131011087844-0.1338404154990.0969698747764-0.458007141519-0.03122311575350.04495737311610.7368642261380.06079256601850.01169138704870.320052581242-0.01083448642990.341211996538-42.533985216131.9023411688-26.0968298668
60.228282797785-0.06916599958320.1107119806020.0329014309492-0.03088477673770.0542686463404-0.0104265773521-0.00699612142727-0.0228112533045-0.03127496690540.02386390509960.00906010418218-0.0113282099885-0.0476758378690.0006897374557460.710542153205-0.1281899033720.00409469737120.658460537562-0.0284592360180.565272988638-38.052243334834.7189442947-19.6259450975
71.22744076443-0.2959712250860.3763833029891.85246359442-0.9949474375180.8803921631510.2188743644130.759154416224-0.11646312062-0.792918833793-0.468621514682-0.3836684196070.2779337419470.6190741877910.2145038338021.003088936280.2361465627740.1448186106631.116664471880.1127885555330.502875143639-10.798676298414.2547153912-54.8699435682
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 0 through 334)AA0 - 3341 - 335
22(chain 'A' and resid 401 through 401)AB401
33(chain 'B' and resid 2 through 334)BC2 - 3341 - 322
44(chain 'B' and resid 401 through 401)BD401
55(chain 'C' and resid 0 through 334)CE0 - 3341 - 335
66(chain 'C' and resid 401 through 401)CF401
77(chain 'D' and resid 2 through 334)DG2 - 3341 - 330

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