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- PDB-4x7p: Crystal structure of apo S. aureus TarM -

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Basic information

Entry
Database: PDB / ID: 4x7p
TitleCrystal structure of apo S. aureus TarM
ComponentsTarM
KeywordsTRANSFERASE / Glycosyltransferase GT-B Retaining Wall teichoic acid
Function / homology
Function and homology information


poly(ribitol-phosphate) alpha-N-acetylglucosaminyltransferase / poly(ribitol-phosphate) N-acetylglucosaminyltransferase activity / teichoic acid biosynthetic process / cell wall organization / cytoplasm
Similarity search - Function
Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(ribitol-phosphate) alpha-N-acetylglucosaminyltransferase / :
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus 21178 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsWorrall, L.J. / Sobhanifar, S. / Gruninger, R.J. / 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: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure and mechanism of Staphylococcus aureus TarM, the wall teichoic acid alpha-glycosyltransferase.
Authors: Sobhanifar, S. / Worrall, L.J. / Gruninger, R.J. / Wasney, G.A. / Blaukopf, M. / Baumann, L. / Lameignere, E. / Solomonson, M. / Brown, E.D. / Withers, S.G. / Strynadka, N.C.
History
DepositionDec 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 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
A: TarM
B: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,26418
Polymers114,7272
Non-polymers1,53716
Water00
1
A: TarM
hetero molecules

A: TarM
hetero molecules

A: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,39727
Polymers172,0913
Non-polymers2,30624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area9190 Å2
ΔGint-338 kcal/mol
Surface area65610 Å2
MethodPISA
2
B: TarM
hetero molecules

B: TarM
hetero molecules

B: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,39727
Polymers172,0913
Non-polymers2,30624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area9060 Å2
ΔGint-323 kcal/mol
Surface area65400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.599, 208.599, 120.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein TarM


Mass: 57363.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus 21178 (bacteria)
Gene: SA21178_0837 / Plasmid: pET41b / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H0AM96, UniProt: A0A0H2WWV6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4

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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: 6.61 Å3/Da / Density % sol: 81.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Na/K tartrate, 100 mM tri-sodium citrate pH 6.5 and 2.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 1, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.4→72.33 Å / Num. obs: 59887 / % possible obs: 100 % / Redundancy: 11 % / Net I/σ(I): 8.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
SCALAdata scaling
PHASERphasing
BUSTERrefinement
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→72.33 Å / Cor.coef. Fo:Fc: 0.9281 / Cor.coef. Fo:Fc free: 0.9123 / SU R Cruickshank DPI: 0.567 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.504 / SU Rfree Blow DPI: 0.27 / SU Rfree Cruickshank DPI: 0.281
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 2100 5.09 %RANDOM
Rwork0.1726 ---
obs0.1733 41264 100 %-
Displacement parametersBiso max: 268.27 Å2 / Biso mean: 101.17 Å2 / Biso min: 20.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.9329 Å20 Å20 Å2
2--4.9329 Å20 Å2
3----9.8658 Å2
Refinement stepCycle: final / Resolution: 3.4→72.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8066 0 80 0 8146
Biso mean--121.98 --
Num. residues----986
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3030SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes242HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1150HARMONIC5
X-RAY DIFFRACTIONt_it8284HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1072SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9412SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8284HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg11128HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion22.63
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2381 142 4.7 %
Rwork0.2231 2880 -
all0.2238 3022 -
obs--100 %
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)
10.45620.01190.23772.2369-0.83500.06710.046-0.10830.2868-0.0952-0.3527-0.1233-0.01090.0281-0.1979-0.0498-0.0056-0.4367-0.0105-0.235-88.009527.59984.0957
20.07760.12020.15481.1106-0.38370.22510.04390.00940.12760.02470.0743-0.02090.14830.0457-0.1182-0.304-0.00810.0468-0.4298-0.1382-0.1709-103.098321.4429-46.4998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|493 }A1 - 493
2X-RAY DIFFRACTION2{ B|1 - B|493 }B1 - 493

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