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- PDB-2ksm: Central B domain of Rv0899 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2ksm
TitleCentral B domain of Rv0899 from Mycobacterium tuberculosis
ComponentsMYCOBACTERIUM TUBERCULOSIS RV0899/MT0922/OmpATb
KeywordsMEMBRANE PROTEIN / OmpATb / BON domain / 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 / simulated annealing, torsion angle dynamics
AuthorsTeriete, P. / Yao, Y. / Kolodzik, A. / Yu, J. / Song, H. / Niederweis, M. / Marassi, F.M.
CitationJournal: Biochemistry / Year: 2010
Title: Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel.
Authors: Teriete, P. / Yao, Y. / Kolodzik, A. / Yu, J. / Song, H. / Niederweis, M. / Marassi, F.M.
History
DepositionJan 7, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYCOBACTERIUM TUBERCULOSIS RV0899/MT0922/OmpATb


Theoretical massNumber of molelcules
Total (without water)13,5421
Polymers13,5421
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)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein MYCOBACTERIUM TUBERCULOSIS RV0899/MT0922/OmpATb


Mass: 13542.272 Da / Num. of mol.: 1 / Fragment: BON domain containing region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv NCTC 7416 / Gene: MT0922, MTCY31.27, Rv0899 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / 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-15N HSQC
123IPAP
1512D 1H-13C HSQC
1613D HNCA
1713D HN(CA)CB
1813D C(CO)NH
1923D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
11313D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.7 mM [U-99% 15N] Rv0899(73-220), 1 mM [U-99% 13C; U-99% 15N] Rv0899(73-220), 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-99% 13C; U-99% 15N] Rv0899(73-220), 0.3 mM [U-99% 15N] Rv0899(73-220), 100% D2O100% D2O
30.4 mM [U-99% 15N] Rv0899(73-220), 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.7 mM15N labeled Rv0899(73-220)[U-99% 15N]1
1.0 mMdouble labeled Rv0899(73-220)[U-99% 13C; U-99% 15N]1
1.0 mMdouble labeled Rv0899(73-220)[U-99% 13C; U-99% 15N]2
0.3 mM15N labeled Rv0899(73-220)[U-99% 15N]2
0.4 mMRv0899(73-220)[U-99% 15N]3
Sample conditionsIonic strength: 0.005 / pH: 7.0 / Pressure: ambient / Temperature: 313 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
NMRPipe3Delaglio, F. et al.processing
Sparky3.115Goddard, T.D. et al.data analysis
TALOSCornilescu, G. et al.chemical shift calculation
X-PLOR NIH2.24Schwieters, C.D. et al.refinement
REDCATValafar, H. et al.rdc analysis
PyMOLDeLano, W.L. et al.structure analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: XPLOR-NIH, XPLOR-NIH internal variable dynamics module (IVM)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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