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

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Basic information

Entry
Database: PDB / ID: 5tze
TitleCrystal structure of S. aureus TarS in complex with UDP-GlcNAc
ComponentsGlycosyl transferaseGlycosyltransferase
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
: / 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: 2.33 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Glycosyl transferase
E: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,34410
Polymers84,6362
Non-polymers1,7098
Water5,747319
1
C: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1725
Polymers42,3181
Non-polymers8544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Glycosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1725
Polymers42,3181
Non-polymers8544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.510, 57.580, 86.480
Angle α, β, γ (deg.)83.810, 82.920, 61.880
Int Tables number1
Space group name H-MP1
DetailsMonomer as determined by SEC-MALS

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Components

#1: Protein Glycosyl transferase / Glycosyltransferase


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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


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


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.11 Å3/Da / Density % sol: 60.4 %
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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→31.43 Å / Num. obs: 39577 / % possible obs: 95 % / Redundancy: 2 % / CC1/2: 0.933 / Rmerge(I) obs: 0.07954 / Net I/σ(I): 9.91
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4743 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.662 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→31.43 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.2333 1821 4.61 %
Rwork0.1891 --
obs0.1912 39508 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.33 Å2 / Biso mean: 42.4907 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 2.33→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 100 319 6087
Biso mean--41.47 40.17 -
Num. residues----698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045880
X-RAY DIFFRACTIONf_angle_d0.6687964
X-RAY DIFFRACTIONf_chiral_restr0.046878
X-RAY DIFFRACTIONf_plane_restr0.0051022
X-RAY DIFFRACTIONf_dihedral_angle_d17.3593528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3301-2.3930.31811710.2572891306296
2.393-2.46340.29511200.23762915303596
2.4634-2.54290.29571280.23682914304295
2.5429-2.63370.27211390.2362908304796
2.6337-2.73910.23921420.22282943308595
2.7391-2.86370.32341280.2152889301796
2.8637-3.01460.29821360.21862948308496
3.0146-3.20330.27591480.20752909305796
3.2033-3.45040.27741030.19112901300495
3.4504-3.79710.2221610.17842812297393
3.7971-4.34540.17541450.14552858300394
4.3454-5.47020.17151710.14992842301395
5.4702-31.84640.19721290.16852957308697
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)
12.15990.5847-0.79831.1560.02342.310.6146-0.98980.47140.5816-0.60130.2183-0.28280.1359-0.02750.5095-0.2530.03850.6069-0.09540.232955.5491-99.1158-84.6532
23.49640.62-1.61234.08790.93745.53090.468-0.31890.26620.0751-0.4250.1935-0.3125-0.2904-0.04970.2392-0.0771-0.03630.3688-0.04670.232452.1619-103.339-93.3829
32.0790.28980.42721.7874-0.2311.57370.083-0.04720.0083-0.0655-0.05950.19750.0648-0.0588-0.02380.18080.05370.01720.1056-0.0190.245140.0566-114.2955-111.2541
42.01930.21950.23181.3759-0.16692.1579-0.36971.28020.2978-0.30450.34930.1904-0.1066-0.02360.01770.3291-0.1358-0.04620.72260.0760.217864.0818-94.1735-142.0286
53.38390.30280.82943.1721-1.50725.6458-0.27980.48960.30560.040.39380.2064-0.436-0.2521-0.10770.2347-0.0476-0.04740.39490.03450.238969.3581-93.0331-133.2855
62.06710.2486-0.22251.63550.75861.4662-0.02410.05510.1523-0.01220.0431-0.0933-0.03680.0667-0.01990.16880.0487-0.02170.1060.03320.23284.7004-87.5265-115.3889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 164 )C1 - 164
2X-RAY DIFFRACTION2chain 'C' and (resid 165 through 217 )C165 - 217
3X-RAY DIFFRACTION3chain 'C' and (resid 218 through 349 )C218 - 351
4X-RAY DIFFRACTION4chain 'E' and (resid 1 through 164 )E1 - 164
5X-RAY DIFFRACTION5chain 'E' and (resid 165 through 217 )E165 - 217
6X-RAY DIFFRACTION6chain 'E' and (resid 218 through 349 )E218 - 351

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