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- PDB-6mpt: TagT bound to LI-WTA -

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Basic information

Entry
Database: PDB / ID: 6mpt
TitleTagT bound to LI-WTA
ComponentsPolyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
KeywordsTRANSFERASE / LytR-Cps2A-Psr / LCP / complex
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / cell wall organization / transferase activity / plasma membrane
Similarity search - Function
Nucleotidyltransferase; domain 5 - #590 / LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C30 / Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.649 Å
AuthorsOwens, T.W. / Schaefer, K. / Kahne, D. / Walker, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM076710 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109764 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066174 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Substrate Preferences Establish the Order of Cell Wall Assembly in Staphylococcus aureus.
Authors: Schaefer, K. / Owens, T.W. / Kahne, D. / Walker, S.
History
DepositionOct 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8893
Polymers32,0631
Non-polymers8252
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.231, 66.231, 140.036
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

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Components

#1: Protein Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT


Mass: 32063.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tagT, ywtF, BSU35840 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7WY78, Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups
#2: Chemical ChemComp-C30 / 2-(acetylamino)-2-deoxy-1-O-[(S)-{[(R)-{[(2Z,6Z,10E,14E,18E)-3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-glucopyranose


Mass: 789.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H65NO12P2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES pH 7.0-7.5, 20-22% w/v PEG 3350, and 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.649→59.872 Å / Num. obs: 38209 / % possible obs: 99.6 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.051 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.683.71.42917870.3550.8141.65597.7
9.03-59.874.50.0252860.9980.0130.02897.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.44 Å59.87 Å
Translation5.44 Å59.87 Å

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASER2.7.15phasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSMay 1, 2016data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DE9

4de9


Resolution: 1.649→59.872 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.99
RfactorNum. reflection% reflection
Rfree0.2215 1907 5 %
Rwork0.1998 --
obs0.2009 38158 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.12 Å2 / Biso mean: 42.8256 Å2 / Biso min: 20.89 Å2
Refinement stepCycle: final / Resolution: 1.649→59.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 117 254 2347
Biso mean--64.42 43.95 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032055
X-RAY DIFFRACTIONf_angle_d0.5262766
X-RAY DIFFRACTIONf_chiral_restr0.042318
X-RAY DIFFRACTIONf_plane_restr0.003352
X-RAY DIFFRACTIONf_dihedral_angle_d15.8391244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6493-1.69050.35741220.33872485260798
1.6905-1.73620.32691170.293225752692100
1.7362-1.78730.31161350.276425622697100
1.7873-1.8450.32131330.261525542687100
1.845-1.9110.3091190.251225672686100
1.911-1.98750.25271360.230825502686100
1.9875-2.07790.25361480.207925812729100
2.0779-2.18750.22991290.215125832712100
2.1875-2.32450.21661330.197925672700100
2.3245-2.5040.19271630.18925802743100
2.504-2.7560.21891380.202626282766100
2.756-3.15480.23771350.198626292764100
3.1548-3.97460.20031360.17522628276499
3.9746-59.91180.20371630.18892762292598

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