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- PDB-8fj9: Structure of the catalytic domain of Streptococcus mutans GtfB in... -

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Basic information

Entry
Database: PDB / ID: 8fj9
TitleStructure of the catalytic domain of Streptococcus mutans GtfB in tetragonal space group P4322
ComponentsGlucosyltransferase-I
KeywordsTRANSFERASE / GtfB / GTF-I / insoluble 1 / 3-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. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glucosyltransferase-I
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,32341
Polymers195,0212
Non-polymers3,30239
Water6,593366
1
A: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,11720
Polymers97,5101
Non-polymers1,60719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucosyltransferase-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,20621
Polymers97,5101
Non-polymers1,69520
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.130, 150.130, 302.783
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, 405 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 71.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2 M ammonium sulfate, 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 EIGER2 S 16M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→86.92 Å / Num. obs: 119867 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.314 / Rpim(I) all: 0.072 / Rrim(I) all: 0.322 / Χ2: 1.01 / Net I/σ(I): 9.3 / Num. measured all: 2410102
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 21 % / Num. unique obs: 5852 / CC1/2: 0.439 / CC star: 0.781 / Rpim(I) all: 0.882 / Χ2: 0.99 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→75.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.165 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24086 6059 5.1 %RANDOM
Rwork0.21216 ---
obs0.21363 113679 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.5→75.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13133 0 175 366 13674
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313594
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712130
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.64418448
X-RAY DIFFRACTIONr_angle_other_deg1.2011.58128199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13851672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36123.825719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91152249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9641561
X-RAY DIFFRACTIONr_chiral_restr0.0520.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022765
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_it3.1935.7916697
X-RAY DIFFRACTIONr_mcbond_other3.1935.7916696
X-RAY DIFFRACTIONr_mcangle_it4.8758.688366
X-RAY DIFFRACTIONr_mcangle_other4.8758.6818367
X-RAY DIFFRACTIONr_scbond_it3.3876.1816897
X-RAY DIFFRACTIONr_scbond_other3.2136.1146790
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1349.049921
X-RAY DIFFRACTIONr_long_range_B_refined7.57667.71414985
X-RAY DIFFRACTIONr_long_range_B_other7.55567.70714963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 27402 / 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: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 406 -
Rwork0.337 8294 -
obs--99.97 %

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