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- PDB-5tzi: Crystal structure of S. aureus TarS 1-349 -

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Basic information

Entry
Database: PDB / ID: 5tzi
TitleCrystal structure of S. aureus TarS 1-349
ComponentsGlycosyl transferase
KeywordsTRANSFERASE / Glycosyltransferase / GT-A / Wall teichoic acid
Function / homology
Function and homology information


poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase / teichoic acid biosynthetic process / hexosyltransferase activity / cell wall organization / response to antibiotic / metal ion binding
Similarity search - Function
TarS beta-glycosyltransferase C-terminal domain 1 / : / TarS beta-glycosyltransferase C-terminal domain 1 / TarS C-terminal domain 2 / : / Glycosyl transferase TarS linker domain / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarS / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWorrall, L.J. / Sobhanifar, S. / King, D.T. / Strynadka, N.C.
CitationJournal: PLoS Pathog. / Year: 2016
Title: Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid beta-glycosyltransferase Involved in Methicillin Resistance.
Authors: Sobhanifar, S. / Worrall, L.J. / King, D.T. / Wasney, G.A. / Baumann, L. / Gale, R.T. / Nosella, M. / Brown, E.D. / Withers, S.G. / Strynadka, N.C.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
C: Glycosyl transferase


Theoretical massNumber of molelcules
Total (without water)42,3181
Polymers42,3181
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.657, 58.656, 86.676
Angle α, β, γ (deg.)90.000, 97.010, 90.000
Int Tables number5
Space group name H-MC121
DetailsMonomer as determined by SEC-MALS

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Components

#1: Protein Glycosyl transferase


Mass: 42317.750 Da / Num. of mol.: 1 / Fragment: residues 2-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: SAMEA2236484_00765, SAMEA2384030_00583, SAMEA2384487_01253, SAMEA2445549_00791, SAMEA2445572_00749, SAMEA2445608_00472, SAMEA2445616_00196, SAMEA2445622_01196, SAMEA2445624_00746, SAMEA2445630_ ...Gene: SAMEA2236484_00765, SAMEA2384030_00583, SAMEA2384487_01253, SAMEA2445549_00791, SAMEA2445572_00749, SAMEA2445608_00472, SAMEA2445616_00196, SAMEA2445622_01196, SAMEA2445624_00746, SAMEA2445630_01744, SAMEA2445663_00417, SAMEA2445672_00193
Production host: Escherichia coli (E. coli)
References: UniProt: A0A181F8T0, UniProt: A0A0H3JPC6*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.2 mM lithium sulfate, 27% w/v PEG 3350, and 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.98 Å / Num. obs: 27265 / % possible obs: 94.7 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.043 / Rrim(I) all: 0.083 / Net I/σ(I): 12.2 / Num. measured all: 100763
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.163.60.7380.756175.5
8.91-44.983.40.0190.999198.4

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Processing

Software
NameVersionClassification
xia2data reduction
Aimless0.5.15data scaling
PHASERphasing
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.976 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.79
RfactorNum. reflection% reflection
Rfree0.2534 1140 5.32 %
Rwork0.2137 --
obs0.2157 21411 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.75 Å2 / Biso mean: 50.9461 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.3→44.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 0 163 2901
Biso mean---46.1 -
Num. residues----337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052792
X-RAY DIFFRACTIONf_angle_d0.6873775
X-RAY DIFFRACTIONf_chiral_restr0.049418
X-RAY DIFFRACTIONf_plane_restr0.005491
X-RAY DIFFRACTIONf_dihedral_angle_d18.3531701
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.40470.30071470.22742525267298
2.4047-2.53150.281430.23512555269898
2.5315-2.69010.33441270.28962386251392
2.6901-2.89770.25721610.23682546270799
2.8977-3.18930.28051500.23252561271199
3.1893-3.65060.26211360.22622501263796
3.6506-4.59870.21561240.18652529265396
4.5987-44.98490.22661520.18622668282099
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)
11.72350.1456-0.24611.24080.18321.4280.14881.1547-0.2941-0.0695-0.0205-0.05490.16360.4164-0.03960.34740.088-0.01330.8759-0.20290.294127.0107112.8641101.7989
21.42990.0240.17710.8963-0.47610.99220.01610.0401-0.01840.0159-0.0334-0.0367-0.05010.01820.01870.226-0.0101-0.01120.1009-0.0560.26957.4634117.5987127.0695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 218 )C1 - 218
2X-RAY DIFFRACTION2chain 'C' and (resid 219 through 348 )C219 - 348

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