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- PDB-6xtt: Solution structure of Legionella pneumophila NttA -

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Basic information

Entry
Database: PDB / ID: 6xtt
TitleSolution structure of Legionella pneumophila NttA
ComponentsNttA
KeywordsUNKNOWN FUNCTION / Legionella pneumophila / Type II Secretion System / Virulence factor
Function / homologyUncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPortlock, T.J. / Garnett, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council1806169 United Kingdom
CitationJournal: Front Mol Biosci / Year: 2020
Title: Structure, Dynamics and Cellular Insight Into Novel Substrates of theLegionella pneumophilaType II Secretion System.
Authors: Portlock, T.J. / Tyson, J.Y. / Dantu, S.C. / Rehman, S. / White, R.C. / McIntire, I.E. / Sewell, L. / Richardson, K. / Shaw, R. / Pandini, A. / Cianciotto, N.P. / Garnett, J.A.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 25, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: NttA


Theoretical massNumber of molelcules
Total (without water)13,3331
Polymers13,3331
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8660 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein NttA


Mass: 13333.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria)
Gene: C3926_06540, C3927_06155, D7214_02725, DI056_01550, DI105_01550, ERS240541_00078, ERS253249_02720, NCTC12000_01505, NCTC12024_01284
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A128USX4, UniProt: Q5ZVQ5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic13D CBCA(CO)NH
132isotropic13D HNCO
142isotropic13D (H)CCH-TOCSY
152isotropic13D CCH-TOCSY
162isotropic13D HNCA
172isotropic13D HN(CO)CA
182isotropic13D HN(CA)CB
192isotropic13D 1H-13C NOESY
1102isotropic13D 1H-15N NOESY
1112isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.4 mM [U-99% 13C; U-99% 15N] NttA, 50 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMNttA[U-99% 13C; U-99% 15N]2
50 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
Sample conditionsIonic strength: 50 mM NaCl, 50 mM sodium phosphate Not defined
Label: Condition1 / pH: 7.0 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 10

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