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

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Basic information

Entry
Database: PDB / ID: 9oue
TitleStructure of full-length Streptococcus mutans GtfD in complex with dextran 5000 in domain V
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / GtfD_FL / domain V / dextran 5000 / 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-D-glucopyranose / 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)151,0015
Polymers146,5291
Non-polymers4,4724
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.300, 94.876, 182.765
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: 146529.109 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 , 3 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-(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-(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-(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-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 3747.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,23,22/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1/a6-b1_b6-c1_c6-d1_d6-e1_e6-f1_f6-g1_g6-h1_h6-i1_i6-j1_j6-k1_k6-l1_l6-m1_m6-n1_n6-o1_o6-p1_p6-q1_q6-r1_r6-s1_s6-t1_t6-u1_u6-v1_v6-w1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 162 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Molecular Dimensions PACT condition #29: 25% PEG 1500, 0.1 M PCB buffer pH 8; 50 mM (final conc.) dextran 5000 (500 mM stock soln. in water) was added to 10.2 mg/ml GtfD-FL (168-1462) for co-crystallization

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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: 2.35→91.38 Å / Num. obs: 64523 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 50 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.059 / Rrim(I) all: 0.164 / Χ2: 1.02 / Net I/σ(I): 9.6
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 7.9 % / Rmerge(I) obs: 2.393 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4494 / CC1/2: 0.458 / Rpim(I) all: 0.903 / Rrim(I) all: 2.561 / Χ2: 1.05

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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→63.5 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 5802 4.73 %Random
Rwork0.2184 ---
obs0.2207 64403 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59 Å2
Refinement stepCycle: LAST / Resolution: 2.35→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10192 0 299 161 10652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510705
X-RAY DIFFRACTIONf_angle_d0.72614493
X-RAY DIFFRACTIONf_dihedral_angle_d15.8451608
X-RAY DIFFRACTIONf_chiral_restr0.051616
X-RAY DIFFRACTIONf_plane_restr0.0051856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.36821750.33043961X-RAY DIFFRACTION99
2.38-2.40.37721360.33713922X-RAY DIFFRACTION100
2.4-2.430.3661720.32953964X-RAY DIFFRACTION100
2.43-2.460.36861950.3273873X-RAY DIFFRACTION100
2.46-2.50.40391990.31793939X-RAY DIFFRACTION100
2.5-2.530.33061990.30693858X-RAY DIFFRACTION100
2.53-2.570.3731990.30743937X-RAY DIFFRACTION100
2.57-2.610.37131860.30623971X-RAY DIFFRACTION100
2.61-2.650.40692110.29773863X-RAY DIFFRACTION100
2.65-2.690.32911870.29843918X-RAY DIFFRACTION100
2.69-2.740.36182140.29623856X-RAY DIFFRACTION100
2.74-2.790.36712060.2833913X-RAY DIFFRACTION100
2.79-2.840.3582270.27453861X-RAY DIFFRACTION100
2.84-2.90.3432050.27693885X-RAY DIFFRACTION99
2.9-2.960.31132350.273872X-RAY DIFFRACTION99
2.96-3.030.32141810.27663920X-RAY DIFFRACTION100
3.03-3.110.33581760.27033856X-RAY DIFFRACTION99
3.11-3.190.35231960.26353796X-RAY DIFFRACTION97
3.19-3.280.31121800.25133939X-RAY DIFFRACTION100
3.28-3.390.32021460.24874020X-RAY DIFFRACTION100
3.39-3.510.32022050.23213861X-RAY DIFFRACTION100
3.51-3.650.31590.2183939X-RAY DIFFRACTION100
3.65-3.820.22281790.19443922X-RAY DIFFRACTION99
3.82-4.020.2261870.18583920X-RAY DIFFRACTION100
4.02-4.270.19522200.1693855X-RAY DIFFRACTION100
4.27-4.60.2042690.16033841X-RAY DIFFRACTION100
4.6-5.060.21741800.16793894X-RAY DIFFRACTION99
5.06-5.790.23862060.18563896X-RAY DIFFRACTION99
5.79-7.30.23421770.18163837X-RAY DIFFRACTION97
7.3-63.50.18531950.16263865X-RAY DIFFRACTION99

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