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- PDB-2ly3: Solution structure of TamA POTRA domain I -

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Basic information

Entry
Database: PDB / ID: 2ly3
TitleSolution structure of TamA POTRA domain I
ComponentsTranslocation and assembly module TamA
KeywordsTRANSPORT PROTEIN / TamA / POTRA / TAM / autotransporter secretion
Function / homology
Function and homology information


TAM protein secretion complex / protein localization to outer membrane / protein secretion / cell outer membrane / plasma membrane
Similarity search - Function
TamA, POTRA domain 1 / POTRA domain TamA domain 1 / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain
Similarity search - Domain/homology
Translocation and assembly module subunit TamA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
AuthorsHeadey, S. / Belousoff, M. / Lithgow, T.
CitationJournal: To be Published
Title: The C-terminal beta-signal-like motif of TamB facilitates efficient autotransporter secretion.
Authors: Selkrig, J. / Headey, S. / Belousoff, M. / Celik, N. / Phan, M. / Schembri, M. / Scanlon, M. / Lithgow, T.
History
DepositionSep 11, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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
1: Translocation and assembly module TamA


Theoretical massNumber of molelcules
Total (without water)10,1581
Polymers10,1581
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translocation and assembly module TamA / Autotransporter assembly factor TamA


Mass: 10157.532 Da / Num. of mol.: 1 / Fragment: C-terminal beta-signal-like motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tamA, yftM, ytfM, b4220, JW4179 / Plasmid: pET-21d / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADE4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1413D CBCA(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D H(CCCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D (H)C(CCO)NH
11213D 1H-13C NOESY aromatic
11312D (HB)CB(CGCD)HD
11412D (HB)CB(CGCDCE)HE
11513D HN(CA)CO

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Sample preparation

DetailsContents: 1.8 mM [U-99% 13C; U-99% 15N] TamA domain I, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.8 mM / Component: TamA domain I-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 70 / pH: 6.4 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
TopSpin3Bruker Biospinprocessing
AtnosCandid2.0.2Herrmann, Guntert and Wuthrichstructure solution
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
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: 10

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