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- PDB-7tod: Solution structure of the phosphatidylinositol 3-phosphate bindin... -

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Basic information

Entry
Database: PDB / ID: 7tod
TitleSolution structure of the phosphatidylinositol 3-phosphate binding domain from the Legionella effector SetA
ComponentsSubversion of eukaryotic traffic protein A
KeywordsLIPID BINDING PROTEIN / phosphatidylinositol-3-phosphate / SetA membrane interacting motif
Function / homologyGlycosyltransferase, DXD sugar-binding motif / Glycosyltransferase sugar-binding region containing DXD motif / Nucleotide-diphospho-sugar transferases / Subversion of eukaryotic traffic protein A
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBeck, W.H.J. / Enoki, T.A. / Feigenson, G.W. / Nicholson, L. / Oswald, R. / Mao, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 R01 GM135379-01 United States
CitationJournal: To Be Published
Title: Solution structure of the phosphatidylinositol 3-phosphate binding domain from the Legionella effector SetA
Authors: Beck, W.H.J. / Enoki, T.A. / Feigenson, G.W. / Nicholson, L. / Oswald, R. / Mao, Y.
History
DepositionJan 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subversion of eukaryotic traffic protein A


Theoretical massNumber of molelcules
Total (without water)12,1931
Polymers12,1931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Subversion of eukaryotic traffic protein A / SetA


Mass: 12192.811 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 522-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_09165
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2S6F4N3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-13C HSQC
141isotropic13D HNCO
151isotropic13D HN(CO)CA
161isotropic13D HNCA
171isotropic13D HN(CA)CB
181isotropic13D HCACO
191isotropic13D CBCA(CO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N-NOESYHSQC
1121isotropic13D 1H-13C-NOESYHSQC (aromatic)
1131isotropic13D 1H-13C-NOESYHSQC (aliphatic)

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Sample preparation

DetailsType: solution
Contents: 6 mg/mL [U-100% 13C; U-100% 15N; U-80% 2H] protein, 20 mM sodium phosphate buffer, 95% H2O/5% D2O
Details: the sample is in 20 mM sodium phosphate buffer pH6.
Label: 13C_15N_sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
6 mg/mLprotein[U-100% 13C; U-100% 15N; U-80% 2H]1
20 mMsodium phosphate buffernatural abundance1
Sample conditionsIonic strength: 20 mM sodium phosphate mM / Label: condition_1 / pH: 6 / PH err: 0.2 / Pressure: 1 atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PONDEROSA-C/SWoonghee Leestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
PONDEROSA-C/SWoonghee Leerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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