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- PDB-4x6l: Crystal structure of S. aureus TarM in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 4x6l
TitleCrystal structure of S. aureus TarM in complex with UDP
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
URIDINE-5'-DIPHOSPHATE / Poly(ribitol-phosphate) alpha-N-acetylglucosaminyltransferase / :
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus 21178 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.19 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 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 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

Downloads & links

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Assembly

Deposited unit
A: TarM
B: TarM
C: TarM
D: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,6677
Polymers229,4554
Non-polymers1,2123
Water00
1
A: TarM
hetero molecules

A: TarM
hetero molecules

A: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3046
Polymers172,0913
Non-polymers1,2123
Water0
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 area6890 Å2
ΔGint-45 kcal/mol
Surface area62660 Å2
MethodPISA
2
B: TarM
hetero molecules

B: TarM
hetero molecules

B: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3046
Polymers172,0913
Non-polymers1,2123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6790 Å2
ΔGint-46 kcal/mol
Surface area62850 Å2
MethodPISA
3
C: TarM
hetero molecules

C: TarM
hetero molecules

C: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3046
Polymers172,0913
Non-polymers1,2123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6830 Å2
ΔGint-44 kcal/mol
Surface area62910 Å2
MethodPISA
4
D: TarM

D: TarM

D: TarM


Theoretical massNumber of molelcules
Total (without water)172,0913
Polymers172,0913
Non-polymers00
Water0
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 area4500 Å2
ΔGint-19 kcal/mol
Surface area63830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.289, 162.289, 228.024
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))
Detailsbiological unit is the same as asym.

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Components

#1: Protein
TarM


Mass: 57363.695 Da / Num. of mol.: 4
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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM

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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: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8-10% w/v PEG 3350, 200 mM NaCl, 200 mM sodium acetate (pH 8.0), 100 mM HEPES (pH 7.0) and 20 % ethylene glycol

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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: 3.19→66.11 Å / Num. obs: 55989 / % possible obs: 99.97 % / Redundancy: 6.7 % / Rsym value: 0.064 / Net I/σ(I): 7.4
Reflection shellResolution: 3.19→3.26 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SHARPphasing
BUSTER-TNTrefinement
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.19→66.11 Å / Cor.coef. Fo:Fc: 0.9514 / Cor.coef. Fo:Fc free: 0.9399 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 2869 5.08 %RANDOM
Rwork0.1653 ---
obs0.1666 55989 99.98 %-
Displacement parametersBiso max: 281.7 Å2 / Biso mean: 120.78 Å2 / Biso min: 49.95 Å2
Baniso -1Baniso -2Baniso -3
1--6.3538 Å20 Å20 Å2
2---6.3538 Å20 Å2
3---12.7076 Å2
Refine analyzeLuzzati coordinate error obs: 0.698 Å
Refinement stepCycle: final / Resolution: 3.19→66.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16132 0 75 0 16207
Biso mean--123.1 --
Num. residues----1972
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6093SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes484HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2327HARMONIC5
X-RAY DIFFRACTIONt_it16518HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2156SEMIHARMONIC5
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_contact18471SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16518HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22184HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion22.39
LS refinement shellResolution: 3.19→3.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2642 214 5.14 %
Rwork0.2365 3946 -
all0.2379 4160 -
obs--99.98 %
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)
11.5432-0.327-0.64881.25590.25070.9950.1186-0.40420.11320.15360.0878-0.5015-0.00220.4849-0.2064-0.1766-0.0461-0.23640.0709-0.0565-0.175535.744290.927-41.7045
20.84410.4679-0.70971.3824-0.67242.0673-0.0002-0.0430.19620.20.1005-0.0888-0.49150.1291-0.1003-0.0348-0.0973-0.1178-0.1508-0.0758-0.130715.184732.3585-4.3393
31.36220.0373-0.95350.4854-0.16871.98730.15270.00720.29070.0570.0178-0.0907-0.45630.4424-0.1704-0.1401-0.1672-0.0631-0.0636-0.0248-0.050829.672120.27-61.328
43.60290.1622-0.69481.83120.06391.7956-0.09610.5059-1.1397-0.34050.001-0.75980.50770.39740.095-0.25660.16760.0743-0.2625-0.15780.019329.603271.9231-97.4041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 493
2X-RAY DIFFRACTION2{ B|* }B1 - 493
3X-RAY DIFFRACTION3{ C|* }C1 - 493
4X-RAY DIFFRACTION4{ D|* }D1 - 493

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