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- PDB-9o9p: Structure of wild type full-length Streptococcus mutans GtfD (GTF-S) -

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Basic information

Entry
Database: PDB / ID: 9o9p
TitleStructure of wild type full-length Streptococcus mutans GtfD (GTF-S)
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / Glucosyltransferase D / GTF-S / 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
Glucosyltransferase-S
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Authors: Schormann, N. / Deivanayagam, C.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 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)161,0052
Polymers160,9651
Non-polymers401
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.113, 94.829, 174.719
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: 160965.156 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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 Å3/Da / Density % sol: 38.8 % / Description: orthorhombic plates and blocks
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Molecular Dimensions LMB #44 condition: 24% PEG3350, 2% PEG400, 0.05M Hepes pH 6.8, 0.15M NaCl

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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: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→64.25 Å / Num. obs: 61235 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 42.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.055 / Rrim(I) all: 0.115 / Χ2: 0.99 / Net I/σ(I): 7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4549 / CC1/2: 0.553 / Rpim(I) all: 0.487 / Rrim(I) all: 0.988 / Χ2: 1.08

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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: 2.25→19.97 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 3042 4.98 %Random
Rwork0.2069 ---
obs0.2097 61078 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.25→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9935 0 1 378 10314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610150
X-RAY DIFFRACTIONf_angle_d0.84413749
X-RAY DIFFRACTIONf_dihedral_angle_d11.1991396
X-RAY DIFFRACTIONf_chiral_restr0.0491464
X-RAY DIFFRACTIONf_plane_restr0.0051815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.34571370.31112656X-RAY DIFFRACTION100
2.29-2.320.3241410.30192639X-RAY DIFFRACTION100
2.32-2.360.32421380.28522653X-RAY DIFFRACTION100
2.36-2.410.36911470.2812619X-RAY DIFFRACTION100
2.41-2.450.31711350.28462664X-RAY DIFFRACTION100
2.45-2.50.37541520.26562616X-RAY DIFFRACTION99
2.5-2.560.32011670.26152570X-RAY DIFFRACTION98
2.56-2.620.31121460.2592495X-RAY DIFFRACTION94
2.62-2.680.29771300.24692644X-RAY DIFFRACTION99
2.68-2.750.33241540.24792611X-RAY DIFFRACTION100
2.75-2.830.33291340.24252682X-RAY DIFFRACTION100
2.83-2.920.33081280.23972689X-RAY DIFFRACTION99
2.92-3.030.28811240.22532651X-RAY DIFFRACTION100
3.03-3.150.26661380.23072704X-RAY DIFFRACTION100
3.15-3.290.25711620.21142620X-RAY DIFFRACTION99
3.29-3.470.29491300.20752655X-RAY DIFFRACTION99
3.47-3.680.26381330.19492649X-RAY DIFFRACTION98
3.68-3.960.23741200.18852577X-RAY DIFFRACTION94
3.96-4.360.2311480.16822672X-RAY DIFFRACTION98
4.36-4.980.21431370.16442656X-RAY DIFFRACTION97
4.98-6.240.22581250.18472633X-RAY DIFFRACTION95
6.24-19.970.20571160.17362681X-RAY DIFFRACTION92

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