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- PDB-5u02: Crystal structure of S. aureus TarS 217-571 -

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Basic information

Entry
Database: PDB / ID: 5u02
TitleCrystal structure of S. aureus TarS 217-571
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 / glycosyltransferase 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 / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
IMIDAZOLE / Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarS / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsWorrall, L.J. / Sobhanifar, S. / King, D.T. / Strynadka, N.C.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
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 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7262
Polymers41,6571
Non-polymers691
Water3,225179
1
A: Glycosyl transferase
hetero molecules

A: Glycosyl transferase
hetero molecules

A: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1776
Polymers124,9703
Non-polymers2073
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6410 Å2
ΔGint-15 kcal/mol
Surface area48670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.690, 105.690, 80.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

21A-761-

HOH

31A-863-

HOH

41A-865-

HOH

51A-873-

HOH

DetailsTrimer as determined by SEC-MALS

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Components

#1: Protein Glycosyl transferase


Mass: 41656.723 Da / Num. of mol.: 1
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 1 M imidazole (pH 7), thermolysin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97881 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 2.31→52.83 Å / Num. obs: 23009 / % possible obs: 98.5 % / Redundancy: 10.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.045 / Rrim(I) all: 0.148 / Net I/σ(I): 18.1 / Num. measured all: 243597 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.31-2.376.71.0371052115730.6410.4211.1231.993.8
10.33-52.8310.10.025298029610.0090.02781.199

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
xia2data reduction
Aimless0.5.23data scaling
autoSHARPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.301→52.83 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 1227 5.33 %
Rwork0.2235 21782 -
obs0.2258 23009 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.25 Å2 / Biso mean: 53.5036 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 2.301→52.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 5 181 3102
Biso mean--52.75 43.84 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042981
X-RAY DIFFRACTIONf_angle_d0.6924018
X-RAY DIFFRACTIONf_chiral_restr0.051442
X-RAY DIFFRACTIONf_plane_restr0.005514
X-RAY DIFFRACTIONf_dihedral_angle_d17.1851800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3005-2.39260.32941350.27112249238493
2.3926-2.50150.33891430.25862409255299
2.5015-2.63340.28981150.257624412556100
2.6334-2.79840.35851190.31382352247195
2.7984-3.01450.2531520.223824312583100
3.0145-3.31790.27091420.218124592601100
3.3179-3.7980.28071520.23782373252597
3.798-4.7850.22181340.19152465259999
4.785-91.60270.23731350.191226032738100
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)
11.3219-0.54-1.29672.26770.82032.7817-0.15291.19170.5931-0.00360.3697-0.14970.38940.0181-0.30660.73340.0777-0.08131.3770.30910.90736.487870.4323-5.496
23.3102-1.0627-0.36651.3175-0.31622.43880.11641.0781.3971-0.02750.0506-0.15760.339-0.0768-0.13540.63880.0118-0.05990.84650.26550.786423.093878.34722.6173
30.1759-0.39010.23350.8665-0.62854.1106-0.23760.87820.495-0.84850.13530.1310.23030.4753-0.01210.6285-0.2318-0.11980.76160.20790.494515.579872.81967.2683
41.6866-0.3052-0.17632.363-0.02321.14330.0810.24130.0546-0.3309-0.04550.1046-0.0388-0.0203-0.00460.23990.0539-0.02470.24530.00180.225812.542358.395826.9824
51.0105-0.4076-0.63090.77380.27762.3996-0.0739-0.152-0.07880.15120.03220.06940.1490.03580.03450.17010.0076-0.00620.164-0.00830.207716.152754.165650.7965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 256 )A217 - 256
2X-RAY DIFFRACTION2chain 'A' and (resid 257 through 337 )A257 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 357 )A338 - 357
4X-RAY DIFFRACTION4chain 'A' and (resid 358 through 445 )A358 - 445
5X-RAY DIFFRACTION5chain 'A' and (resid 446 through 571 )A446 - 571

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