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- PDB-8fk4: Structure of the catalytic domain of Streptococcus mutans GtfB co... -

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Basic information

Entry
Database: PDB / ID: 8fk4
TitleStructure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in orthorhombic space group P21212
ComponentsGlucosyltransferase-I
KeywordsTRANSFERASE / GtfB / GTF-I / insoluble 1 / 3-linked alpha glucans / biofilm / streptococcus mutans / 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
alpha-acarbose / Glucosyltransferase-I
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 20, 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
B: Glucosyltransferase-I
C: Glucosyltransferase-I
D: Glucosyltransferase-I
E: Glucosyltransferase-I
F: Glucosyltransferase-I
G: Glucosyltransferase-I
H: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)789,50865
Polymers780,0848
Non-polymers9,42457
Water905
1
A: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7739
Polymers97,5101
Non-polymers1,2628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,86910
Polymers97,5101
Non-polymers1,3589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6768
Polymers97,5101
Non-polymers1,1667
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6768
Polymers97,5101
Non-polymers1,1667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,86910
Polymers97,5101
Non-polymers1,3589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7739
Polymers97,5101
Non-polymers1,2628
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5807
Polymers97,5101
Non-polymers1,0706
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2924
Polymers97,5101
Non-polymers7823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)299.312, 215.766, 219.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 97510.484 Da / Num. of mol.: 8 / 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
#2: Polysaccharide
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 4.54 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulfate, 0.1 M Bis-Tris; the complex was obtained by co-crystallization with a 1:10 molar ratio of acarbose (final concentration 1-2 mM)
PH range: 5.5

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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: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→49.44 Å / Num. obs: 222519 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 99.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.076 / Rrim(I) all: 0.199 / Χ2: 1.02 / Net I/σ(I): 7.4
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 10910 / CC1/2: 0.394 / CC star: 0.752 / Rpim(I) all: 0.972 / Χ2: 1.04

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.16_3549refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→48.882 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 11040 4.97 %
Rwork0.2236 --
obs0.2252 222189 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→48.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52044 0 565 5 52614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253687
X-RAY DIFFRACTIONf_angle_d0.54372912
X-RAY DIFFRACTIONf_dihedral_angle_d4.1732089
X-RAY DIFFRACTIONf_chiral_restr0.0418049
X-RAY DIFFRACTIONf_plane_restr0.0049446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.28690.4043420.37667015X-RAY DIFFRACTION100
3.2869-3.32560.36663480.3657032X-RAY DIFFRACTION100
3.3256-3.36610.35543820.35246950X-RAY DIFFRACTION100
3.3661-3.40870.38323810.34986961X-RAY DIFFRACTION100
3.4087-3.45360.38923930.33876950X-RAY DIFFRACTION100
3.4536-3.50090.34923640.32166964X-RAY DIFFRACTION100
3.5009-3.55090.34483700.31226994X-RAY DIFFRACTION100
3.5509-3.60390.32073740.29247016X-RAY DIFFRACTION100
3.6039-3.66020.30643820.28556987X-RAY DIFFRACTION100
3.6602-3.72010.34383790.28686998X-RAY DIFFRACTION100
3.7201-3.78430.32073650.28386964X-RAY DIFFRACTION100
3.7843-3.85310.30463760.26896985X-RAY DIFFRACTION100
3.8531-3.92710.29223940.25486997X-RAY DIFFRACTION100
3.9271-4.00730.26453410.24487058X-RAY DIFFRACTION100
4.0073-4.09430.2613460.22847008X-RAY DIFFRACTION100
4.0943-4.18950.25143640.22146976X-RAY DIFFRACTION100
4.1895-4.29430.25813410.22617055X-RAY DIFFRACTION100
4.2943-4.41030.26243700.21387040X-RAY DIFFRACTION100
4.4103-4.540.23623640.20656992X-RAY DIFFRACTION100
4.54-4.68640.2543670.20677064X-RAY DIFFRACTION100
4.6864-4.85380.24193780.20027014X-RAY DIFFRACTION100
4.8538-5.04790.23233770.19777077X-RAY DIFFRACTION100
5.0479-5.27740.22463540.19537033X-RAY DIFFRACTION100
5.2774-5.55530.22083280.19737130X-RAY DIFFRACTION100
5.5553-5.90280.25063920.2037070X-RAY DIFFRACTION100
5.9028-6.35760.20933690.19927098X-RAY DIFFRACTION100
6.3576-6.99580.22583830.19237126X-RAY DIFFRACTION100
6.9958-8.00420.21663600.17757127X-RAY DIFFRACTION100
8.0042-10.070.17124030.15527195X-RAY DIFFRACTION100
10.07-48.8820.21873530.19557273X-RAY DIFFRACTION97

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