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

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Basic information

Entry
Database: PDB / ID: 9ogx
TitleStructure of full-length Streptococcus mutans GtfD active site mutant (D465A, D584A) in complex with sucrose
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 / Glucosyltransferase-S
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 2, 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)161,6244
Polymers160,8771
Non-polymers7473
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.441, 96.993, 181.557
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
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.: 2
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-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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Molecular Dimensions condition LMB #44: 24% PEG3350, 2% PEG 400, 0.05M Hepes pH6.8, 0.15M NaCl; apo crystals were soaked with 50mM sucrose (final; 1M stock solution in water)

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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: 2.85→83.44 Å / Num. obs: 24970 / % possible obs: 72.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 92.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.047 / Rrim(I) all: 0.105 / Χ2: 1.06 / Net I/σ(I): 9.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.671 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3729 / CC1/2: 0.391 / Rpim(I) all: 0.841 / Rrim(I) all: 1.885 / Χ2: 1.02 / % possible all: 75.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→75.93 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.885 / SU B: 38.698 / SU ML: 0.689 / Cross valid method: THROUGHOUT / ESU R Free: 0.68 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32558 1265 5.1 %RANDOM
Rwork0.27761 ---
obs0.2801 23691 70.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.213 Å2
Baniso -1Baniso -2Baniso -3
1-2.93 Å2-0 Å2-0 Å2
2---6.78 Å20 Å2
3---3.85 Å2
Refinement stepCycle: 1 / Resolution: 2.85→75.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9703 0 50 0 9753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0129970
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169025
X-RAY DIFFRACTIONr_angle_refined_deg0.8541.80313490
X-RAY DIFFRACTIONr_angle_other_deg0.3511.77520742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50751228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.929532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45101631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0430.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022407
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1589.8994948
X-RAY DIFFRACTIONr_mcbond_other2.1589.8994948
X-RAY DIFFRACTIONr_mcangle_it3.68117.7866164
X-RAY DIFFRACTIONr_mcangle_other3.68117.7876165
X-RAY DIFFRACTIONr_scbond_it1.7199.8765022
X-RAY DIFFRACTIONr_scbond_other1.7199.8765023
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.10418.1827327
X-RAY DIFFRACTIONr_long_range_B_refined5.86194.3411591
X-RAY DIFFRACTIONr_long_range_B_other5.86194.3311592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 89 -
Rwork0.416 1793 -
obs--74.33 %

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