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- PDB-9oub: Structure of full-length Streptococcus mutans GtfD in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9oub
TitleStructure of full-length Streptococcus mutans GtfD in complex with dextran 1000 in domain V
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / GtfD_FL / domain V / dextran 1000 / 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: 2.35 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 28, 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)162,8057
Polymers160,9651
Non-polymers1,8406
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.841, 95.485, 175.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1a_1-5]/1-1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 66 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: apo crystals of GtfD-FL in Molecular Dimensions LMB condition #44 (24% PEG 3350, 2% PEG 400, 0.05 M Hepes PH 6.8, 0.15 M NaCl) were soaked with 10 mM (final conc.) of dextran 1000 (100 mM stock soln. 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 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→84.47 Å / Num. obs: 58878 / % possible obs: 97.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.061 / Rrim(I) all: 0.162 / Χ2: 0.95 / Net I/σ(I): 6.4
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 7 % / Rmerge(I) obs: 2.24 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4576 / CC1/2: 0.408 / Rpim(I) all: 0.909 / Rrim(I) all: 2.421 / Χ2: 0.84

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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: 2.35→64.58 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2842 2577 4.92 %Random
Rwork0.2382 ---
obs0.2405 52346 94.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.35→64.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10056 0 119 63 10238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310381
X-RAY DIFFRACTIONf_angle_d0.70514049
X-RAY DIFFRACTIONf_dihedral_angle_d12.9671477
X-RAY DIFFRACTIONf_chiral_restr0.0441521
X-RAY DIFFRACTIONf_plane_restr0.0041832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.34541340.32462709X-RAY DIFFRACTION94
2.4-2.440.36541620.32492675X-RAY DIFFRACTION94
2.44-2.50.39381370.31952756X-RAY DIFFRACTION95
2.5-2.560.41781360.31462706X-RAY DIFFRACTION94
2.56-2.620.34311220.30882666X-RAY DIFFRACTION92
2.62-2.690.32351660.27282823X-RAY DIFFRACTION98
2.69-2.770.32821400.26812829X-RAY DIFFRACTION98
2.77-2.860.29881520.26622840X-RAY DIFFRACTION98
2.86-2.960.31191510.27152818X-RAY DIFFRACTION98
2.96-3.080.32421280.26782878X-RAY DIFFRACTION97
3.08-3.220.36351620.27982758X-RAY DIFFRACTION97
3.22-3.390.31571530.26782787X-RAY DIFFRACTION96
3.39-3.60.33011300.25252722X-RAY DIFFRACTION94
3.6-3.880.29561350.23012631X-RAY DIFFRACTION89
3.88-4.270.25911330.20722769X-RAY DIFFRACTION94
4.27-4.890.24661430.18932782X-RAY DIFFRACTION94
4.89-6.160.19321260.19852807X-RAY DIFFRACTION93
6.16-64.580.20751670.18592813X-RAY DIFFRACTION90

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