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- PDB-6uf6: Crystal structure of B. subtilis TagU -

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Basic information

Entry
Database: PDB / ID: 6uf6
TitleCrystal structure of B. subtilis TagU
ComponentsPolyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU
KeywordsTRANSFERASE / LytR / CpsA / Psr
Function / homology
Function and homology information


cell wall assembly / phosphotransferase activity, for other substituted phosphate groups / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU / LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3378
Polymers30,6691
Non-polymers6687
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU
hetero molecules

A: Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,67516
Polymers61,3382
Non-polymers1,33714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4200 Å2
ΔGint-151 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.792, 48.792, 234.271
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagU / Membrane-bound protein LytR


Mass: 30668.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: tagU, lytR, BSU35650 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02115, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→42.255 Å / Num. obs: 17406 / % possible obs: 99.58 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 16.23
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 1686 / CC1/2: 0.897 / % possible all: 99.11

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→42.255 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.36
RfactorNum. reflection% reflection
Rfree0.2588 864 4.98 %
Rwork0.2445 --
obs0.2452 17338 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 172.33 Å2 / Biso mean: 93.2892 Å2 / Biso min: 53.59 Å2
Refinement stepCycle: final / Resolution: 2.2→42.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 36 5 1806
Biso mean--129.37 73.06 -
Num. residues----231
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.33790.37171380.3584266499
2.3379-2.51840.34611410.31992667100
2.5184-2.77180.3331390.3173267999
2.7718-3.17280.30711450.27442732100
3.1728-3.99690.29231450.25172783100
3.9969-42.2550.21051560.21292949100
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)
14.72191.5630.90956.70111.73526.5025-0.31620.03360.01250.28310.18621.35190.61330.07040.1190.93520.22650.11120.68430.0350.47946.793211.198120.1842
27.80671.7495-5.5532.07792.59875.46120.2747-1.7821-0.33821.8481-0.616-1.1864-1.12331.41560.11811.44550.1037-0.12171.542-0.07540.579418.12816.934130.2648
35.7729-3.0457-0.72242.3533-0.3322.877-0.1841-0.44830.71740.21910.39670.28160.00790.6618-0.29161.21290.25460.19410.6598-0.08070.4535-1.160725.918819.3887
48.2906-0.0699-5.81691.42922.48198.0143-0.015-0.063-0.14560.82970.05520.2328-0.41710.2547-0.13690.98360.23970.12810.40620.0220.42643.106621.952911.9602
57.8931-1.2833-7.29999.357-0.12398.8443-0.22440.3608-0.28380.10490.3616-0.2195-0.16260.48830.07270.93140.17140.03810.8503-0.07770.393510.233715.86248.6196
62.9891.90143.74654.24080.89214.55880.3576-1.02580.05771.2097-0.71830.31580.9329-0.92570.18831.03130.23780.30551.14380.09050.82484.131914.648133.4978
73.9171-0.02830.34626.13174.4266.00830.1633-0.6785-0.36251.1832-0.81521.13230.0254-1.07990.39111.46730.36150.4210.75130.23490.81767.7081-1.606227.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 44 )A4 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 81 )A45 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 145 )A82 - 145
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 181 )A146 - 181
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 196 )A182 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 229 )A197 - 229
7X-RAY DIFFRACTION7chain 'A' and (resid 230 through 250 )A230 - 250

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