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- PDB-9oih: Structure of full-length Streptococcus mutans GtfD active site mu... -

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Basic information

Entry
Database: PDB / ID: 9oih
TitleStructure of full-length Streptococcus mutans GtfD active site mutant (D465A, D584A) with active site glucose
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / GtfD_FL / active site mutant / Dextransucrase
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / extracellular region
Similarity search - Function
Glucan-binding repeat / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
sucrose / alpha-D-glucopyranose / Glucosyltransferase-S
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSchormann, N. / Deivanayagam, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1R01DE033232-01A1 United States
CitationJournal: To Be Published
Title: Structural and Functional Analysis of Streptococcus mutans GtfD-FL (GTF-S)
Authors: Schormann, N. / Deivanayagam, C.
History
DepositionMay 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosyltransferase-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5025
Polymers160,8771
Non-polymers6254
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.007, 97.309, 182.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucosyltransferase-S / GTF-S / Dextransucrase / Sucrose 6-glucosyltransferase


Mass: 160877.125 Da / Num. of mol.: 1 / Mutation: D465A, D584A
Source method: isolated from a genetically manipulated source
Details: The active site mutant structure of GtfD-FL contains glucose in the active site and sucrose in domain V.
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: gtfD, SMU_910 / Plasmid: pET-21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49331, dextransucrase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Molecular Dimension LMB screen #44: 24% PEG 3350, 2% PEG 400, 0.05M Hepes pH 6.8, 0.15M NaCl; apo crystals of mutant GtfD-FL were soaked with 50mM sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→85.9 Å / Num. obs: 25581 / % possible obs: 96.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 86.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.092 / Rrim(I) all: 0.255 / Χ2: 0.97 / Net I/σ(I): 7.9
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.327 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4616 / CC1/2: 0.483 / Rpim(I) all: 0.954 / Rrim(I) all: 2.527 / Χ2: 0.93

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→60.06 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1296 5.11 %random
Rwork0.2494 ---
obs0.2519 25357 95.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85 Å2
Refinement stepCycle: LAST / Resolution: 3.15→60.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10073 0 40 0 10113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210322
X-RAY DIFFRACTIONf_angle_d0.48713974
X-RAY DIFFRACTIONf_dihedral_angle_d12.0833741
X-RAY DIFFRACTIONf_chiral_restr0.041484
X-RAY DIFFRACTIONf_plane_restr0.0031832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.280.36041470.33442530X-RAY DIFFRACTION92
3.28-3.430.38381340.34212615X-RAY DIFFRACTION95
3.43-3.610.41121190.31342732X-RAY DIFFRACTION97
3.61-3.830.34951450.27852690X-RAY DIFFRACTION97
3.83-4.130.30981510.26332676X-RAY DIFFRACTION97
4.13-4.540.25421450.22112683X-RAY DIFFRACTION96
4.54-5.20.30051520.22232664X-RAY DIFFRACTION95
5.2-6.550.28251480.25152693X-RAY DIFFRACTION95
6.55-60.060.26061550.21272778X-RAY DIFFRACTION93

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