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- PDB-8fg8: Catalytic domain of GtfB in complex with inhibitor 2-[(2,4,5-Trih... -

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Basic information

Entry
Database: PDB / ID: 8fg8
TitleCatalytic domain of GtfB in complex with inhibitor 2-[(2,4,5-Trihydroxyphenyl)methylidene]-1-benzofuran-3-one
ComponentsGlucosyltransferase-I
KeywordsTRANSFERASE/INHIBITOR / GtfB / GTF-I / catalytic domain / inhibitor / TRANSFERASE-INHIBITOR complex
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
Chem-XV5 / Glucosyltransferase-I
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSchormann, N. / Deivanayagam, C. / Velu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)DE028349 United States
CitationJournal: J.Med.Chem. / Year: 2023
Title: Hydrogel-Encapsulated Biofilm Inhibitors Abrogate the Cariogenic Activity of Streptococcus mutans .
Authors: Ahirwar, P. / Kozlovskaya, V. / Nijampatnam, B. / Rojas, E.M. / Pukkanasut, P. / Inman, D. / Dolmat, M. / Law, A.C. / Schormann, N. / Deivanayagam, C. / Harber, G.J. / Michalek, S.M. / Wu, H. ...Authors: Ahirwar, P. / Kozlovskaya, V. / Nijampatnam, B. / Rojas, E.M. / Pukkanasut, P. / Inman, D. / Dolmat, M. / Law, A.C. / Schormann, N. / Deivanayagam, C. / Harber, G.J. / Michalek, S.M. / Wu, H. / Kharlampieva, E. / Velu, S.E.
History
DepositionDec 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucosyltransferase-I
B: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,40633
Polymers195,0212
Non-polymers3,38531
Water9,062503
1
A: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,99114
Polymers97,5101
Non-polymers1,48013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,41519
Polymers97,5101
Non-polymers1,90518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.455, 150.455, 304.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 97510.484 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 191-1051)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: gtfB, SMU_1004 / Plasmid: pET-23d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08987, dextransucrase

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Non-polymers , 5 types, 534 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XV5 / (2Z)-2-[(2,4,5-trihydroxyphenyl)methylidene]-1-benzofuran-3(2H)-one


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.42 Å3/Da / Density % sol: 72.2 % / Description: Tetragonal rods
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2 M ammonium sulfate, 0.1 M Bis-Tris, apo- crystals soaked 5-10 mins with inhibitor HA5 (20 mM aqueous stock solution; 1-2 mM final concentration)

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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: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→87.25 Å / Num. obs: 142674 / % possible obs: 98.5 % / Redundancy: 9.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.065 / Rrim(I) all: 0.202 / Χ2: 0.98 / Net I/σ(I): 8.1 / Num. measured all: 1293084
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 9.3 % / Num. unique obs: 7062 / CC1/2: 0.35 / Rpim(I) all: 0.712 / Χ2: 0.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSVersion Mar 15, 2019data reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3AIE

3aie


Resolution: 2.35→73.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.384 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23255 6850 4.9 %RANDOM
Rwork0.20544 ---
obs0.20675 133011 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.35→73.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13055 0 191 503 13749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313541
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712061
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.64418388
X-RAY DIFFRACTIONr_angle_other_deg1.2131.58728042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40251660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22323.774718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.348152241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6071562
X-RAY DIFFRACTIONr_chiral_restr0.0570.21761
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022770
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4715.5686652
X-RAY DIFFRACTIONr_mcbond_other3.4715.5686651
X-RAY DIFFRACTIONr_mcangle_it5.2278.3438308
X-RAY DIFFRACTIONr_mcangle_other5.2278.3448309
X-RAY DIFFRACTIONr_scbond_it3.826.0316888
X-RAY DIFFRACTIONr_scbond_other3.6155.9716793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7058.8019937
X-RAY DIFFRACTIONr_long_range_B_refined8.18665.09314846
X-RAY DIFFRACTIONr_long_range_B_other8.14265.06114782
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 26613 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 521 -
Rwork0.336 9835 -
obs--97.61 %

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