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- PDB-4x7r: Crystal structure of S. aureus TarM G117R mutant in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4x7r
TitleCrystal structure of S. aureus TarM G117R mutant in complex with Fondaparinux, alpha-GlcNAc-glycerol and 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
fondaparinux / Chem-3YW / URIDINE-5'-DIPHOSPHATE / 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: 2.15 Å
AuthorsWorrall, L.J. / Sobhanifar, S. / 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 25, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 12, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity_src_gen / pdbx_struct_oper_list / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_site_gen.auth_seq_id
Revision 2.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 2.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,3438
Polymers114,9282
Non-polymers4,4156
Water6,575365
1
A: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6724
Polymers57,4641
Non-polymers2,2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-15 kcal/mol
Surface area23170 Å2
MethodPISA
2
B: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6724
Polymers57,4641
Non-polymers2,2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-15 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.470, 92.140, 96.110
Angle α, β, γ (deg.)65.890, 83.660, 84.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TarM /


Mass: 57463.836 Da / Num. of mol.: 2 / Mutation: G117R
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: Polysaccharide 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside / fondaparinux /


Type: oligosaccharide, Oligosaccharide / Class: Anticoagulant / Mass: 1508.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: fondaparinux
DescriptorTypeProgram
WURCS=2.0/5,5,4/[a2122h-1a_1-5_1*OC_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2121A-1a_1-5_2*OSO/3=O/3=O][a2122h-1a_1-5_2*NSO/3=O/3=O_3*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O]/1-2-3-4-5/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-GlcpNSO36SO3]{[(4+1)][a-L-IdopA2SO3]{[(4+1)][a-D-GlcpNSO33SO36SO3]{[(4+1)][b-D-GlcpA]{[(4+1)][a-D-GlcpNSO36SO3]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar ChemComp-3YW / (2S)-2,3-dihydroxypropyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside / (2S)-2,3-dihydroxypropyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside / (2S)-2,3-dihydroxypropyl 2-acetamido-2-deoxy-alpha-D-glucoside / (2S)-2,3-dihydroxypropyl 2-acetamido-2-deoxy-D-glucoside / (2S)-2,3-dihydroxypropyl 2-acetamido-2-deoxy-glucoside


Type: D-saccharide / Mass: 295.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H21NO8
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 MES pH 6.5, 10-14 % w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.033 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 22, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→87.48 Å / Num. obs: 71890 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.045 / Net I/σ(I): 9.1 / Num. measured all: 276850 / Scaling rejects: 78
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.15-2.22.80.5051.61303045840.7370.37696.7
10.31-87.483.80.04920.825236570.9950.0398.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
Aimless0.3.6data scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→87.48 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9402 / SU R Cruickshank DPI: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 3707 5.16 %RANDOM
Rwork0.1792 ---
obs0.1803 71885 97.87 %-
Displacement parametersBiso max: 182.34 Å2 / Biso mean: 58.09 Å2 / Biso min: 25.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.3942 Å23.294 Å23.6011 Å2
2---5.8058 Å2-4.5802 Å2
3---3.4115 Å2
Refinement stepCycle: final / Resolution: 2.15→87.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8080 0 272 365 8717
Biso mean--53.83 53.6 -
Num. residues----986
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3150SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes242HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1176HARMONIC5
X-RAY DIFFRACTIONt_it8516HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1144SEMIHARMONIC5
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_contact9821SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8516HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11484HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion17.62
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2047 240 4.57 %
Rwork0.1884 5010 -
all0.1892 5250 -
obs--97.87 %
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)
10.5296-0.19350.73020.6935-0.80252.6274-0.0026-0.12640.10830.14370.055-0.0336-0.4003-0.0963-0.0524-0.1652-0.0590.0303-0.05810.0823-0.09977.1552-1.468-88.8684
20.48480.3908-0.23831.5717-1.37562.02790.01530.1048-0.1239-0.2851-0.0582-0.02310.32810.02940.0429-0.1785-0.004-0.0143-0.00040.0579-0.1643-7.246843.9156-57.155
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 493
2X-RAY DIFFRACTION2{ B|* }B1 - 493

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