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- PDB-5tzj: Crystal structure of S. aureus TarS 1-349 in complex with UDP-GlcNAc -

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Basic information

Entry
Database: PDB / ID: 5tzj
TitleCrystal structure of S. aureus TarS 1-349 in complex with UDP-GlcNAc
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
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarS / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8504
Polymers84,6362
Non-polymers1,2152
Water6,557364
1
C: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9252
Polymers42,3181
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9252
Polymers42,3181
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.002, 57.370, 86.786
Angle α, β, γ (deg.)83.030, 84.550, 62.260
Int Tables number1
Space group name H-MP1
DetailsMonomer as determined by SEC-MALS

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Components

#1: Protein Glycosyl transferase


Mass: 42317.750 Da / Num. of mol.: 2 / 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: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 60.22 %
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: 0.984 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: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.9→48.56 Å / Num. obs: 71901 / % possible obs: 94.6 % / Redundancy: 2 % / Biso Wilson estimate: 27.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.062 / Rrim(I) all: 0.088 / Net I/σ(I): 7.6 / Num. measured all: 143292
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.9-1.9420.8570.396193.8
9.31-48.5620.0240.997195.3

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Processing

Software
NameVersionClassification
xia2data reduction
Aimless0.5.15data scaling
PHASERphasing
PHENIX(1.10_2155)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.558 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.45
RfactorNum. reflection% reflection
Rfree0.2265 3595 5 %
Rwork0.1894 --
obs0.1913 71872 94.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106 Å2 / Biso mean: 38.7272 Å2 / Biso min: 13.02 Å2
Refinement stepCycle: final / Resolution: 1.9→48.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 78 364 6110
Biso mean--40.56 41.71 -
Num. residues----698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145871
X-RAY DIFFRACTIONf_angle_d1.2227951
X-RAY DIFFRACTIONf_chiral_restr0.071879
X-RAY DIFFRACTIONf_plane_restr0.0081024
X-RAY DIFFRACTIONf_dihedral_angle_d18.0883535
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9250.44571340.37592551268593
1.925-1.95140.42651360.33632587272394
1.9514-1.97930.31621410.30072673281495
1.9793-2.00880.28781380.27572615275395
2.0088-2.04020.32761430.25782735287896
2.0402-2.07370.32141320.24722496262892
2.0737-2.10940.27431420.23262696283895
2.1094-2.14780.26871360.21212581271796
2.1478-2.18910.25881410.20172693283496
2.1891-2.23380.24721370.20682606274395
2.2338-2.28230.25521400.20822660280093
2.2823-2.33540.23741370.20112596273395
2.3354-2.39380.27941410.18652686282796
2.3938-2.45860.21141400.1872654279495
2.4586-2.53090.23981390.19132630276995
2.5309-2.61260.24631400.19182667280795
2.6126-2.7060.20181370.18932597273494
2.706-2.81430.2461390.192645278495
2.8143-2.94230.23411390.19252626276595
2.9423-3.09750.24441390.19022630276995
3.0975-3.29150.21161370.18662610274794
3.2915-3.54550.19111360.17352590272693
3.5455-3.90220.20951350.16232560269593
3.9022-4.46650.17721370.14842613275094
4.4665-5.6260.19551390.16232635277495
5.626-48.57340.18591400.17542645278595
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)
11.64570.3101-0.69222.020.01573.99440.4031-0.50130.2730.5487-0.511-0.047-0.30650.07740.05170.4764-0.20710.00540.4975-0.07360.222667.5756-89.4865-85.9822
23.8060.9209-0.42113.16911.60613.18080.2892-0.41070.1650.4764-0.39130.21920.0757-0.31860.06180.3463-0.10890.02860.3425-0.04430.193356.8801-102.1869-89.4943
32.06070.75420.08271.8756-0.55011.13250.0166-0.00770.14510.032-0.00520.17990.0278-0.0324-0.00610.13930.03270.02530.1054-0.03770.220147.5974-110.6225-112.3953
41.10450.364-0.02412.7004-0.72183.4712-0.39650.90130.1298-0.42430.52460.61450.1245-0.69-0.14170.383-0.2021-0.09960.70310.12350.332663.683-91.6374-142.8801
53.35470.74250.96643.6215-1.39074.0337-0.36130.62630.314-0.18190.31310.0196-0.20560.09830.04660.273-0.0813-0.00180.39820.02180.20179.9096-88.1266-139.4365
62.71160.3458-0.42921.40310.17021.2837-0.01430.02030.17510.00460.0279-0.09030.0210.0371-0.01690.14410.0321-0.00960.09840.0210.221191.7498-83.9152-116.5934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 99 )C1 - 99
2X-RAY DIFFRACTION2chain 'C' and (resid 100 through 217 )C100 - 217
3X-RAY DIFFRACTION3chain 'C' and (resid 218 through 349 )C218 - 349
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 99 )A1 - 99
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 217 )A100 - 217
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 349 )A218 - 349

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