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- PDB-4x7m: Crystal structure of S. aureus TarM G117R mutant in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4x7m
TitleCrystal structure of S. aureus TarM G117R mutant in complex with UDP and UDP-GlcNAc
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-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / 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: 2.4 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 1.0Mar 4, 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 22, 2017Group: Refinement description / Structure summary / Category: entity / software / Item: _entity.pdbx_description / _software.classification
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 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)115,9394
Polymers114,9282
Non-polymers1,0122
Water1,06359
1
A: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8682
Polymers57,4641
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TarM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0712
Polymers57,4641
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.072, 90.944, 94.441
Angle α, β, γ (deg.)109.270, 99.030, 101.530
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: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
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: 0.978 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 1, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→46.04 Å / Num. obs: 49087 / % possible obs: 95.3 % / Redundancy: 2 % / Biso Wilson estimate: 63.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.031 / Net I/σ(I): 16.3 / Num. measured all: 97880
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.480.4482918045980.7640.44896.5
9.6-46.040.01357.514837540.9990.01392.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
Aimless0.3.6data scaling
PHASERphasing
BUSTERrefinement
REFMACrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.04 Å / Cor.coef. Fo:Fc: 0.9303 / Cor.coef. Fo:Fc free: 0.9039 / SU R Cruickshank DPI: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.272
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 2518 5.13 %RANDOM
Rwork0.2326 ---
obs0.2348 49081 95.33 %-
Displacement parametersBiso max: 208.27 Å2 / Biso mean: 90.2 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.9251 Å2-1.0907 Å2-9.8565 Å2
2--2.2187 Å21.8612 Å2
3---0.7064 Å2
Refine analyzeLuzzati coordinate error obs: 0.642 Å
Refinement stepCycle: final / Resolution: 2.4→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8058 0 64 59 8181
Biso mean--69.42 50.18 -
Num. residues----986
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2924 187 5.08 %
Rwork0.2624 3495 -
all0.2639 3682 -
obs--95.33 %
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)
10.98090.74680.05045.45061.23541.19530.4144-0.19180.3831.1355-0.40280.59040.1224-0.0309-0.0116-0.1318-0.13830.2727-0.2409-0.1785-0.1741-0.2399-65.3756-36.4899
21.3987-1.9139-1.8715.40074.89656.9410.26070.0839-0.3378-0.9914-0.65630.5222-0.6216-0.36430.39560.09520.1576-0.2372-0.3144-0.1305-0.1942-7.5928-24.1657-65.8811
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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