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- PDB-9ojh: Structure of full-length Streptococcus mutans GtfD with inhibitor... -

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Basic information

Entry
Database: PDB / ID: 9ojh
TitleStructure of full-length Streptococcus mutans GtfD with inhibitor maltose in active site
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / GtfD_FL / active site maltose / 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-maltose / Glucosyltransferase-S
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

Downloads & links

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Assembly

Deposited unit
A: Glucosyltransferase-S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,4104
Polymers160,9651
Non-polymers4443
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.390, 99.121, 177.129
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: Polysaccharide alpha-D-glucopyranose-(1-4)-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 / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+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: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Molecular Dimensions LMB screen #44: 24% PEG 3350, 2% PEG 400, 0.05M Hepes pH 6.8, 0.15M NaCl; apo crystals were soaked with 10mM maltose.

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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: Oct 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→88.56 Å / Num. obs: 77767 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 42.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.05 / Rrim(I) all: 0.154 / Χ2: 1.03 / Net I/σ(I): 8.9
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 9.8 % / Rmerge(I) obs: 2.242 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4580 / CC1/2: 0.616 / Rpim(I) all: 0.748 / Rrim(I) all: 2.367 / Χ2: 1.09

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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: 2.15→50.73 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 3875 4.99 %Random
Rwork0.2255 ---
obs0.2276 77675 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10101 0 28 362 10491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310354
X-RAY DIFFRACTIONf_angle_d0.73714009
X-RAY DIFFRACTIONf_dihedral_angle_d7.8081423
X-RAY DIFFRACTIONf_chiral_restr0.0491482
X-RAY DIFFRACTIONf_plane_restr0.0041837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.43591510.36482624X-RAY DIFFRACTION100
2.18-2.20.36231300.34152605X-RAY DIFFRACTION100
2.2-2.230.32551260.33432626X-RAY DIFFRACTION100
2.23-2.260.37081450.31862541X-RAY DIFFRACTION100
2.26-2.30.3671360.31682633X-RAY DIFFRACTION100
2.3-2.330.34921460.31552585X-RAY DIFFRACTION100
2.33-2.370.36451440.31032615X-RAY DIFFRACTION100
2.37-2.410.30881250.29222589X-RAY DIFFRACTION100
2.41-2.450.35231340.2962623X-RAY DIFFRACTION100
2.45-2.490.30071360.27962596X-RAY DIFFRACTION100
2.49-2.540.35171380.27852643X-RAY DIFFRACTION100
2.54-2.590.29481110.27592623X-RAY DIFFRACTION100
2.59-2.650.31591390.2762594X-RAY DIFFRACTION100
2.65-2.710.34371450.26692610X-RAY DIFFRACTION100
2.71-2.780.31021370.27072663X-RAY DIFFRACTION100
2.78-2.850.31051210.26142607X-RAY DIFFRACTION100
2.85-2.940.32241370.25972614X-RAY DIFFRACTION100
2.94-3.030.31371440.25592626X-RAY DIFFRACTION100
3.03-3.140.2881490.25992611X-RAY DIFFRACTION100
3.14-3.260.27251360.24972652X-RAY DIFFRACTION100
3.26-3.410.28771440.2372636X-RAY DIFFRACTION100
3.41-3.590.25941230.22482641X-RAY DIFFRACTION100
3.59-3.820.25461440.20532675X-RAY DIFFRACTION100
3.82-4.110.2481270.22670X-RAY DIFFRACTION100
4.11-4.530.22231440.17262666X-RAY DIFFRACTION100
4.53-5.180.20951480.16552680X-RAY DIFFRACTION100
5.18-6.520.23911430.192725X-RAY DIFFRACTION100
6.52-50.730.20081720.17542827X-RAY DIFFRACTION100

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