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- PDB-6fw4: Protein-protein interactions and conformational changes : Importa... -

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Basic information

Entry
Database: PDB / ID: 6fw4
TitleProtein-protein interactions and conformational changes : Importance of the hydrophobic cavity of TolA C-terminal domain
ComponentsTolA protein
KeywordsPROTEIN BINDING / complex / induced fit / conformation / vibrio / cholerae / pressure / viral / phage / interaction / TolA / pIII / G3P / cavitie / protein
Function / homology
Function and homology information


transporter activity / bacteriocin transport / toxin transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
TolA C-terminal / Tol-Pal system, TolA / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 / Fusion Protein Consisting Of Minor Coat Protein, Glycine Rich Linker, Tola, And A His Tag; Chain: A; Domain 2 - #10 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TolA protein / TolA protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodSOLUTION NMR / distance geometry / molecular dynamics
AuthorsNavarro, R. / van Heijenoort, C. / Bornet, O. / Houot, L. / Lloubes, R. / Guerlesquin, F. / Nouailler, M.
CitationJournal: To Be Published
Title: Induced fit conformational changes of Vibrio cholerae TolAIII domain during the complex formation with the viral PIIIN1 domain: Structural and High-pressure NMR studies.
Authors: Navarro, R. / van Heijenoort, C. / Bornet, O. / Houot, L. / Lloubes, R. / Guerlesquin, F. / Nouailler, M.
History
DepositionMar 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: database_2 / pdbx_database_related
Item: _database_2.database_code / _pdbx_database_related.db_id
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TolA protein


Theoretical massNumber of molelcules
Total (without water)11,0101
Polymers11,0101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6610 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein TolA protein


Mass: 11009.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013140_01933 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H6WQ38, UniProt: Q9KR10*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
142isotropic12D 1H-15N HSQC
152isotropic12D 1H-1H TOCSY
162isotropic12D 1H-1H COSY
172isotropic12D 1H-13C CBCACO
1102isotropic13D HNCO
192isotropic13D HN(CA)CB
182isotropic13D CBCA(CO)NH
1112isotropic13D (H)CCH-TOCSY
2122isotropic32D 1H-15N HSQC
2132isotropic22D 1H-15N HSQC
1142isotropic33D 1H-15N NOESY
1152isotropic33D 1H-15N TOCSY
1162isotropic33D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM TolAIII, 90% H2O/10% D2O1H_sample90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] TolAIII, 90% H2O/10% D2O15N_13C_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTolAIIInatural abundance1
0.5 mMTolAIII[U-13C; U-15N]2
Sample conditions

Ionic strength: 0.5 M / Ionic strength err: 0.05 / pH: 6.9 / PH err: 0.1 / Temperature: 300 K / Temperature err: 5

Conditions-IDLabelPressure (kPa)Pressure err
1conditions_11 bar
2HP_conditions2500 bar10

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AvanceIIIBrukerAvanceIII6001IMM platform
Bruker AvanceIIIBrukerAvanceIII9502TGIR Gif sur Yvette
Bruker AvanceIIIBrukerAvanceIII8003TGIR Gif sur Yvette

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospindata analysis
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinal
distance geometry6
molecular dynamics5
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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