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- PDB-9oji: Structure of Streptococcus mutans GtfD with C-terminally truncate... -

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Basic information

Entry
Database: PDB / ID: 9oji
TitleStructure of Streptococcus mutans GtfD with C-terminally truncated domain V in complex with acarbose
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / GtfD_FL / active site acarbose / 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
alpha-acarbose / 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 7, 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)127,4223
Polymers126,7361
Non-polymers6862
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.289, 94.588, 174.167
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: 126736.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Molecular Dimensions PACT screen #29: 25% PEG 1500, 0.1M PCB buffer pH 8; the GtfD construct (168-1287) was co-crystallized with acarbose (final conc. 50mM).

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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: Apr 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→79.29 Å / Num. obs: 22720 / % possible obs: 97.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 73.9 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.134 / Rrim(I) all: 0.273 / Χ2: 0.57 / Net I/σ(I): 3.3
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.695 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4120 / CC1/2: 0.489 / Rpim(I) all: 0.966 / Rrim(I) all: 1.963 / Χ2: 0.57

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→60.76 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3067 1091 4.81 %Random
Rwork0.2546 ---
obs0.257 22675 97.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69 Å2
Refinement stepCycle: LAST / Resolution: 3.15→60.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8554 0 45 30 8629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028769
X-RAY DIFFRACTIONf_angle_d0.42511879
X-RAY DIFFRACTIONf_dihedral_angle_d4.3121214
X-RAY DIFFRACTIONf_chiral_restr0.0381281
X-RAY DIFFRACTIONf_plane_restr0.0031557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.290.41241330.35862703X-RAY DIFFRACTION99
3.29-3.470.3891450.32972697X-RAY DIFFRACTION99
3.47-3.680.36521470.28542657X-RAY DIFFRACTION97
3.68-3.970.33071480.25682645X-RAY DIFFRACTION97
3.97-4.370.27881460.22572692X-RAY DIFFRACTION99
4.37-50.27771370.20812737X-RAY DIFFRACTION98
5-6.30.2821140.24492752X-RAY DIFFRACTION97
6.3-60.760.25911210.23862701X-RAY DIFFRACTION91

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