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- PDB-2lez: Solution NMR structure of N-terminal domain of Salmonella effecto... -

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Basic information

Entry
Database: PDB / ID: 2lez
TitleSolution NMR structure of N-terminal domain of Salmonella effector protein PipB2. Northeast structural genomics consortium (NESG) target stt318a
ComponentsSecreted effector protein pipB2
KeywordsSIGNALING PROTEIN / Structural Genomics / Northeast Structural Genomics Consortium / NESG / BACTERIAL EFFECTOR / VIRULENCE FACTOR / PSI-Biology
Function / homology
Function and homology information


host cell membrane / extracellular region / membrane
Similarity search - Function
Secreted effector protein pipB2 / : / Secreted effector protein PipB2, N-terminal domain / Secreted effector protein pipB2 fold / : / Pentapeptide repeats (8 copies) / Pentapeptide repeat / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Secreted effector protein PipB2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest energy, model 1
AuthorsLemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Daniels, C. / Savchenko, A. / Arrowsmith, C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR solution structure of N-terminal domain of Salmonella effector protein PipB2
Authors: Lemak, A. / Yee, A. / Houliston, S. / Garcia, M. / Daniels, C. / Savchenko, A. / Montelione, G.T. / Arrowsmith, C.
History
DepositionJun 27, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted effector protein pipB2


Theoretical massNumber of molelcules
Total (without water)15,9111
Polymers15,9111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Secreted effector protein pipB2 / Type III effector pipB2


Mass: 15911.110 Da / Num. of mol.: 1 / Fragment: sequence database residues 17-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: pipB2, STM2780 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZMM8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZnSO4, 10 mM DTT, 0.01 % NaN3, 10 mM benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMprotein-1[U-13C; U-15N]1
10 mMTRIS-21
300 mMsodium chloride-31
10 uMZnSO4-41
10 mMDTT-51
0.01 %NaN3-61
10 mMbenzamidine-71
Sample conditionsIonic strength: 300 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
FMCLemak,Steren,Llinas, Arrowsmithchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionevalidation
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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