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- PDB-8fn5: Structure of the truncated catalytic domain of Streptococcus muta... -

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Basic information

Entry
Database: PDB / ID: 8fn5
TitleStructure of the truncated catalytic domain of Streptococcus mutans GtfD
ComponentsGlucosyltransferase-S
KeywordsTRANSFERASE / GtfD / GTF-S / soluble 1 / 6-linked alpha glucans / biofilm / glucansucrase
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: 1.92 Å
AuthorsSchormann, N. / Deivanayagam, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis.
Authors: Schormann, N. / Patel, M. / Thannickal, L. / Purushotham, S. / Wu, R. / Mieher, J.L. / Wu, H. / Deivanayagam, C.
History
DepositionDec 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosyltransferase-S
B: Glucosyltransferase-S


Theoretical massNumber of molelcules
Total (without water)141,2082
Polymers141,2082
Non-polymers00
Water7,044391
1
A: Glucosyltransferase-S


Theoretical massNumber of molelcules
Total (without water)70,6041
Polymers70,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosyltransferase-S


Theoretical massNumber of molelcules
Total (without water)70,6041
Polymers70,6041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.625, 126.765, 173.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucosyltransferase-S / GTF-S / Dextransucrase / Sucrose 6-glucosyltransferase


Mass: 70604.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Crystal structure shows a truncated catalytic domain of GtfD. The initial purified construct stretches from 248 to 1090. Proteolysis occurred during crystallization, and resulted in the ...Details: Crystal structure shows a truncated catalytic domain of GtfD. The initial purified construct stretches from 248 to 1090. Proteolysis occurred during crystallization, and resulted in the residue range of 423-1054.
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 26% PEG 2000MME, 0.1 M Bis-Tris

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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: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→86.83 Å / Num. obs: 97783 / % possible obs: 95.6 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.057 / Rrim(I) all: 0.116 / Χ2: 1.01 / Net I/σ(I): 7.7
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4973 / CC1/2: 0.657 / CC star: 0.891 / Rpim(I) all: 0.469 / Rrim(I) all: 0.93 / Χ2: 1.05 / % possible all: 98.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→86.83 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.85 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 4821 4.9 %RANDOM
Rwork0.226 ---
obs0.2272 92899 95.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.67 Å2 / Biso mean: 31.257 Å2 / Biso min: 15.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0.02 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.92→86.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9364 0 0 391 9755
Biso mean---30.84 -
Num. residues----1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168864
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.6412945
X-RAY DIFFRACTIONr_angle_other_deg1.1931.59120427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48151190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0724.851505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59151654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3061532
X-RAY DIFFRACTIONr_chiral_restr0.0530.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022196
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 375 -
Rwork0.37 6984 -
all-7359 -
obs--98.16 %

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