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- PDB-6uf3: Crystal structure of B. subtilis TagV -

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Basic information

Entry
Database: PDB / ID: 6uf3
TitleCrystal structure of B. subtilis TagV
ComponentsPolyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagV
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
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 TagV
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 TagV


Theoretical massNumber of molelcules
Total (without water)30,8241
Polymers30,8241
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.994, 66.104, 81.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30823.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: tagV, yvhJ, BSU35520 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P96499, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.93 Å3/Da / Density % sol: 36.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.3 M ammonium nitrate, 17% 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: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→36.643 Å / Num. obs: 30022 / % possible obs: 99.82 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.06274 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.456 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2963 / CC1/2: 0.709

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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: 3NXH

3nxh


Resolution: 1.6→36.643 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.61
RfactorNum. reflection% reflection
Rfree0.2288 1500 5 %
Rwork0.2004 --
obs0.2018 29994 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.11 Å2 / Biso mean: 36.2288 Å2 / Biso min: 14.38 Å2
Refinement stepCycle: final / Resolution: 1.6→36.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 167 2133
Biso mean---42.53 -
Num. residues----254
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.65170.34731340.32772553100
1.6517-1.71070.35671340.30072549100
1.7107-1.77920.30191340.26922557100
1.7792-1.86020.29381350.24512551100
1.8602-1.95820.24661340.2142555100
1.9582-2.08090.21611350.19852566100
2.0809-2.24150.23271360.19382567100
2.2415-2.46710.23591360.18872596100
2.4671-2.8240.22511380.19382612100
2.824-3.55740.23681380.18112628100
3.5574-36.6430.19081460.1889276099
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)
14.7210.86430.33772.94540.31852.7219-0.04520.05290.246-0.041-0.09270.2739-0.0776-0.23780.1030.12790.01530.02260.1164-0.00950.160425.392244.469427.6437
23.79080.916-1.4732.6279-1.30843.1604-0.10940.4774-0.0426-0.3359-0.0065-0.1995-0.0060.03060.04430.2115-0.0084-0.0020.2282-0.03070.255237.947252.793917.1614
32.61671.75070.5973.240.83031.6762-0.0222-0.0211-0.29210.0441-0.0115-0.16760.06030.04430.04490.13120.02650.02270.15860.00880.183732.726140.81427.944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 155 )A72 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 262 )A156 - 262
3X-RAY DIFFRACTION3chain 'A' and (resid 263 through 332 )A263 - 332

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