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- PDB-6uf5: Crystal structure of B. subtilis TagT -

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Basic information

Entry
Database: PDB / ID: 6uf5
TitleCrystal structure of B. subtilis TagT
ComponentsPolyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
KeywordsTRANSFERASE / LytR / CpsA / Psr
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / cell wall organization / transferase activity / plasma membrane
Similarity search - Function
Nucleotidyltransferase; domain 5 - #590 / LCP protein / : / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLi, F.K.K. / Strynadka, N.C.J.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystallographic analysis ofStaphylococcus aureusLcpA, the primary wall teichoic acid ligase.
Authors: Li, F.K.K. / Rosell, F.I. / Gale, R.T. / Simorre, J.P. / Brown, E.D. / Strynadka, N.C.J.
History
DepositionSep 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT


Theoretical massNumber of molelcules
Total (without water)33,7791
Polymers33,7791
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.656, 65.656, 143.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT


Mass: 33779.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: tagT, ywtF, BSU35840 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q7WY78, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium malonate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97964 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 2.8→48.371 Å / Num. obs: 8240 / % possible obs: 99.84 % / Redundancy: 13.9 % / CC1/2: 0.997 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.55 / Num. unique obs: 795 / CC1/2: 0.655

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DE9

4de9


Resolution: 2.8→48.371 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.18
RfactorNum. reflection% reflection
Rfree0.2795 410 4.98 %
Rwork0.2308 --
obs0.2333 8230 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.62 Å2 / Biso mean: 63.125 Å2 / Biso min: 28.76 Å2
Refinement stepCycle: final / Resolution: 2.8→48.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 0 2 1881
Biso mean---43.66 -
Num. residues----245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.8002-3.20530.35611330.27082525
3.2053-4.0380.2481340.22822573
4.038-48.3710.27891430.22172722
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4483-0.53720.8312.081-0.10231.5109-0.079-0.15220.039-0.10280.08470.1162-0.1017-0.250.01910.3123-0.01490.02670.43090.02740.4967-14.980811.5828-3.9029
28.1758-3.27140.51685.09682.50532.314-0.13470.04050.5542-0.273-0.0014-0.4769-0.4455-0.04580.19030.47530.0194-0.02260.49750.03650.439-4.58177.27633.7459
33.3652-0.59680.87544.4504-1.36462.47310.2492-0.0774-0.18740.009-0.2109-0.2582-0.01610.1532-0.03850.3808-0.054-0.03320.5595-0.16230.477-12.410610.173-10.7729
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 202 )A52 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 243 )A203 - 243
3X-RAY DIFFRACTION3chain 'A' and (resid 244 through 322 )A244 - 322

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