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- PDB-9o9q: Structure of full-length Streptococcus mutans GtfD active site mu... -

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Basic information

Entry
Database: PDB / ID: 9o9q
TitleStructure of full-length Streptococcus mutans GtfD active site mutant (D465S, D584S)
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
Glucosyltransferase-S
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
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)161,0113
Polymers160,9091
Non-polymers1022
Water17,096949
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.389, 99.284, 177.514
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: 160909.125 Da / Num. of mol.: 1 / Mutation: D465S, D584S
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: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
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: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→88.76 Å / Num. obs: 120947 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 27.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.045 / Rrim(I) all: 0.109 / Χ2: 1.03 / Net I/σ(I): 9.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.368 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5948 / CC1/2: 0.531 / Rpim(I) all: 0.619 / Rrim(I) all: 1.504 / Χ2: 1.08

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→51.09 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 5941 4.92 %Random
Rwork0.194 ---
obs0.1961 120840 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→51.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10140 0 5 949 11094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110381
X-RAY DIFFRACTIONf_angle_d1.1114052
X-RAY DIFFRACTIONf_dihedral_angle_d14.7333770
X-RAY DIFFRACTIONf_chiral_restr0.0651481
X-RAY DIFFRACTIONf_plane_restr0.0081849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.3111850.27593826X-RAY DIFFRACTION100
1.87-1.890.30421690.27593807X-RAY DIFFRACTION100
1.89-1.920.34061840.27243843X-RAY DIFFRACTION100
1.92-1.940.31452200.2613720X-RAY DIFFRACTION99
1.94-1.970.29731880.25453858X-RAY DIFFRACTION100
1.97-1.990.31061890.25623810X-RAY DIFFRACTION100
1.99-2.020.30691880.24813816X-RAY DIFFRACTION100
2.02-2.050.31032170.23933775X-RAY DIFFRACTION100
2.05-2.080.26311990.22953790X-RAY DIFFRACTION100
2.08-2.120.26762080.21363805X-RAY DIFFRACTION99
2.12-2.150.23711700.20983784X-RAY DIFFRACTION99
2.15-2.190.24941840.21093724X-RAY DIFFRACTION97
2.19-2.240.25882130.21173792X-RAY DIFFRACTION99
2.24-2.280.29841840.21413821X-RAY DIFFRACTION100
2.28-2.330.25372060.20843797X-RAY DIFFRACTION100
2.33-2.390.28922000.19953797X-RAY DIFFRACTION100
2.39-2.440.24622160.19723829X-RAY DIFFRACTION100
2.44-2.510.25052190.19453844X-RAY DIFFRACTION100
2.51-2.580.29232200.19753802X-RAY DIFFRACTION100
2.58-2.670.24492080.20513845X-RAY DIFFRACTION100
2.67-2.760.24531700.20083885X-RAY DIFFRACTION100
2.76-2.870.27571810.20423860X-RAY DIFFRACTION100
2.87-30.25761900.19923844X-RAY DIFFRACTION99
3-3.160.25422050.20883733X-RAY DIFFRACTION97
3.16-3.360.23462230.20043865X-RAY DIFFRACTION99
3.36-3.620.20491740.18523881X-RAY DIFFRACTION99
3.62-3.990.21911950.17153915X-RAY DIFFRACTION100
3.99-4.560.19342000.15193898X-RAY DIFFRACTION99
4.56-5.750.18062310.16213908X-RAY DIFFRACTION99
5.75-51.090.19422050.17514025X-RAY DIFFRACTION97

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