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- PDB-2kgs: Solution structure of the amino-terminal domain of OmpATb, a pore... -

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Basic information

Entry
Database: PDB / ID: 2kgs
TitleSolution structure of the amino-terminal domain of OmpATb, a pore forming protein from Mycobacterium tuberculosis
ComponentsUncharacterized protein Rv0899/MT0922
KeywordsMEMBRANE PROTEIN / outer membrane protein A / Mycobacterium tuberculosis / BON Domain / Cell membrane / Membrane / Transmembrane
Function / homology
Function and homology information


response to host pH environment / ammonium transmembrane transport / peptidoglycan binding / cell wall / response to acidic pH / porin activity / plasma membrane => GO:0005886 / monoatomic ion transport / peptidoglycan-based cell wall / cell outer membrane ...response to host pH environment / ammonium transmembrane transport / peptidoglycan binding / cell wall / response to acidic pH / porin activity / plasma membrane => GO:0005886 / monoatomic ion transport / peptidoglycan-based cell wall / cell outer membrane / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
hypothetical protein tt1634 - #20 / hypothetical protein tt1634 / BON domain / BON domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...hypothetical protein tt1634 - #20 / hypothetical protein tt1634 / BON domain / BON domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan-binding protein ArfA / Peptidoglycan-binding protein ArfA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, minimization
Model detailslowest energy, model 1
AuthorsYang, Y. / Auguin, D. / Delbecq, S. / Dumas, E. / Molle, V. / Saint, N.
CitationJournal: Proteins / Year: 2011
Title: Structure of the Mycobacterium tuberculosis OmpATb protein: A model of an oligomeric channel in the mycobacterial cell wall
Authors: Yang, Y. / Auguin, D. / Delbecq, S. / Dumas, E. / Molle, G. / Molle, V. / Roumestand, C. / Saint, N.
History
DepositionMar 18, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Rv0899/MT0922


Theoretical massNumber of molelcules
Total (without water)13,6131
Polymers13,6131
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein Rv0899/MT0922 / OmpATb / outer membrane protein A OMPA


Mass: 13613.350 Da / Num. of mol.: 1 / Fragment: 13.6kDa amino-terminal fragment, residues 73-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0899, MT0922, MTCY31.27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)omp8 / References: UniProt: P65593, UniProt: P9WIU5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-15N HSQC
1313D 1H-15N NOESY
1413D HNCO
1513D HNCA
1613D CBCA(CO)NH
1713D 1H-13C NOESY
1812D 1H-15N HSQC
2912D 1H-1H NOESY

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Sample preparation

DetailsContents: 50 mM sodium phosphate-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 50 mM / Component: sodium phosphate-1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 6 ambient 300 K
2100 ambient 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
GifaDelsucprocessing
XwinNMRBruker Biospincollection
RefinementMethod: DGSA-distance geometry simulated annealing, minimization
Software ordinal: 1 / Details: Cyana, Amber
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10 / Representative conformer: 1

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