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- PDB-1s62: Solution structure of the Escherichia coli TolA C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1s62
TitleSolution structure of the Escherichia coli TolA C-terminal domain
ComponentsTolA protein
KeywordsPROTEIN TRANSPORT / tol g3p interaction
Function / homology
Function and homology information


cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell division site / disordered domain specific binding / symbiont entry into host cell / cell cycle ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell division site / disordered domain specific binding / symbiont entry into host cell / cell cycle / protein domain specific binding / cell division / membrane / plasma membrane
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
Tol-Pal system protein TolA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / 2 step simulated annealing torsion angle dynamics
AuthorsDeprez, C. / Blanchard, L. / Simorre, J.-P. / Gavioli, M. / Guerlesquin, F. / Lazdunski, C. / Lloubes, R. / Marion, D.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Solution structure of the E.coli TolA C-terminal domain reveals conformational changes upon binding to the phage g3p N-terminal domain.
Authors: Deprez, C. / Lloubes, R. / Gavioli, M. / Marion, D. / Guerlesquin, F. / Blanchard, L.
History
DepositionJan 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TolA protein


Theoretical massNumber of molelcules
Total (without water)11,3301
Polymers11,3301
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)16 / 1000structures with the lowest energy
RepresentativeModel #3closest to the average

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Components

#1: Protein TolA protein


Mass: 11329.827 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 325-421)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TOLA, CIM, EXCC, LKY, B0739 / Plasmid: pTolAIII3 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P19934

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2223D 13C-separated NOESY
3333D 15N-separated NOESY
NMR detailsText: NOE mixing time of 0.08 s, triple-resonance probe including shielded z-gradients

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM U-15N, 100mN NaCl, 50mM NaPO4, 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM U-15N,13C, 50mN NaCl, 50mM NaPO4, Complete protease inhibitor (Boehringer), 90% H2O, 10% D2O90% H2O/10% D2O
30.7mM U-15N, 500mN NaCl, 50mM NaPO4, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mN NaCl, 50mM NaPO4 6.8 ambient 300 K
250mN NaCl, 50mM NaPO4 6.8 ambient 300 K
3500mN NaCl, 50mM NaPO4 6.8 ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMRvariancollection
Felix2000Accelrysprocessing
Felix2000Accelrysdata analysis
ARIA1Nilgesstructure solution
TALOSCornilescustructure solution
TALOSCornilescurefinement
RefinementMethod: 2 step simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 16

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