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- PDB-8uf5: Catalytic domain of GtfB in complex with inhibitor G43 -

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Basic information

Entry
Database: PDB / ID: 8uf5
TitleCatalytic domain of GtfB in complex with inhibitor G43
ComponentsGlucosyltransferase-I
KeywordsCELL ADHESION / 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-WIJ / Glucosyltransferase-I
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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: Sci Rep / Year: 2017
Title: Structure-Based Discovery of Small Molecule Inhibitors of Cariogenic Virulence.
Authors: Zhang, Q. / Nijampatnam, B. / Hua, Z. / Nguyen, T. / Zou, J. / Cai, X. / Michalek, S.M. / Velu, S.E. / Wu, H.
History
DepositionOct 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: 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-I
B: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,98117
Polymers195,0212
Non-polymers1,96015
Water6,972387
1
A: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2936
Polymers97,5101
Non-polymers7835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,68811
Polymers97,5101
Non-polymers1,17710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.777, 149.777, 304.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 212 through 215 or resid 218...
21(chain B and (resid 212 through 259 or (resid 262...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALARGARG(chain A and (resid 212 through 215 or resid 218...AA212 - 21522 - 25
12LEULEULEULEU(chain A and (resid 212 through 215 or resid 218...AA21828
13TYRTYRTYRTYR(chain A and (resid 212 through 215 or resid 218...AA21929
14ASNASNILEILE(chain A and (resid 212 through 215 or resid 218...AA208 - 104718 - 857
15ASNASNILEILE(chain A and (resid 212 through 215 or resid 218...AA208 - 104718 - 857
16ASNASNILEILE(chain A and (resid 212 through 215 or resid 218...AA208 - 104718 - 857
17ASNASNILEILE(chain A and (resid 212 through 215 or resid 218...AA208 - 104718 - 857
21VALVALTHRTHR(chain B and (resid 212 through 259 or (resid 262...BB212 - 25922 - 69
22THRTHRTHRTHR(chain B and (resid 212 through 259 or (resid 262...BB26272
23VALVALSERSER(chain B and (resid 212 through 259 or (resid 262...BB212 - 104822 - 858
24VALVALSERSER(chain B and (resid 212 through 259 or (resid 262...BB212 - 104822 - 858
25VALVALSERSER(chain B and (resid 212 through 259 or (resid 262...BB212 - 104822 - 858
26VALVALSERSER(chain B and (resid 212 through 259 or (resid 262...BB212 - 104822 - 858

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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 , 7 types, 402 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-WIJ / N-(2-carbamoylphenyl)-5-nitro-1-benzothiophene-2-carboxamide


Mass: 341.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


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


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 4.37 Å3/Da / Density % sol: 71.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2 M Ammonium sulfate, 0.1 M Bis-Tris, pH 5.5; apo crystals soaked 5-10 mins with inhibitor G43 (100 mM stock solution in DMSO; 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 EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→86.9 Å / Num. obs: 119912 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.066 / Rrim(I) all: 0.242 / Net I/σ(I): 11.8 / Num. measured all: 1571524 / Scaling rejects: 633
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.402 / Num. unique obs: 5836 / CC1/2: 0.563 / Rpim(I) all: 0.423 / Rrim(I) all: 1.465 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.17_3644refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→56.35 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 6049 5.05 %
Rwork0.1992 113721 -
obs0.2007 119770 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.3 Å2 / Biso mean: 43.6556 Å2 / Biso min: 13.25 Å2
Refinement stepCycle: final / Resolution: 2.5→56.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13140 0 120 387 13647
Biso mean--62.75 41.01 -
Num. residues----1670
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5000X-RAY DIFFRACTION5.565TORSIONAL
12B5000X-RAY DIFFRACTION5.565TORSIONAL
LS refinement shellResolution: 2.5→2.53 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3368 177 -
Rwork0.2874 3736 -
obs--100 %

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