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- PDB-8fkl: Truncated form of the catalytic domain of Streptococcus mutans GtfB -

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Basic information

Entry
Database: PDB / ID: 8fkl
TitleTruncated form of the catalytic domain of Streptococcus mutans GtfB
ComponentsGlucosyltransferase-I
KeywordsTRANSFERASE / GtfB (GTF-I) / biofilm / streptococcus mutans / insoluble 1 / 3-linked alpha glucans / 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. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glucosyltransferase-I
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 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 21, 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-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6803
Polymers57,5931
Non-polymers862
Water8,665481
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.671, 90.862, 92.256
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-I / GTF-I / Dextransucrase / Sucrose 6-glucosyltransferase


Mass: 57593.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Constitutes a truncated (proteolysed) version of the catalytic domain of Streptococcus mutans at high resolution.
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: gtfB, SMU_1004 / Plasmid: pET-23d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08987, dextransucrase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / 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.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 61 % / Description: block-like
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 20% PEG 8000, 0.2 M magnesium chloride, 0.1 M Caps

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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 EIGER2 S 16M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→92.26 Å / Num. obs: 121563 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Χ2: 0.98 / Net I/σ(I): 13.6
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 7 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5970 / CC1/2: 0.861 / CC star: 0.925 / Rpim(I) all: 0.255 / Rrim(I) all: 0.677 / Χ2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→64.74 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.029 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17 5865 4.8 %RANDOM
Rwork0.1415 ---
obs0.1428 115647 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.75 Å2 / Biso mean: 27.777 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.4 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 1.48→64.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 5 481 4431
Biso mean--37.51 40.32 -
Num. residues----506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173805
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.6385514
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5888739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.18523.486218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98315678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2151521
X-RAY DIFFRACTIONr_chiral_restr0.0610.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02946
X-RAY DIFFRACTIONr_rigid_bond_restr0.89537870
LS refinement shellResolution: 1.48→1.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 471 -
Rwork0.211 8444 -
all-8915 -
obs--100 %

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