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- PDB-2k0l: NMR structure of the transmembrane domain of the Outer Membrane P... -

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Basic information

Entry
Database: PDB / ID: 2k0l
TitleNMR structure of the transmembrane domain of the Outer Membrane Protein A from Klebsiella pneumoniae in DHPC micelles.
ComponentsOuter membrane protein A
KeywordsMEMBRANE PROTEIN / OMPA / TROSY / sidechain / DHPC micelles
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Porin - #20 / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Porin - #20 / 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. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein A
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing, torsion angle dynamics
AuthorsRenault, M. / Saurel, O. / Gervais, V. / Lohr, F. / Reat, V. / Piotto, M. / Milon, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications.
Authors: Renault, M. / Saurel, O. / Czaplicki, J. / Demange, P. / Gervais, V. / Lohr, F. / Reat, V. / Piotto, M. / Milon, A.
History
DepositionFeb 4, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Outer membrane protein A


Theoretical massNumber of molelcules
Total (without water)23,3951
Polymers23,3951
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer membrane protein A / Outer membrane protein II


Mass: 23394.812 Da / Num. of mol.: 1 / Fragment: transmembrane domain
Source method: isolated from a genetically manipulated source
Details: @ / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: RV 308 / Description: protein expressed in inclusion bodies. / Gene: ompA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P24017

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D [15N,1H]-TROSY
1213D [15N,1H]-TROSY-HN(CA)CB
1313D [15N,1H]-TROSY-HN(CO)CACB
1413D [15N,1H]-TROSY-HNCO
1513D [15N,1H]-TROSY-HN(CA)CO
1613D (HNCA)CC-TOCSY-(CA)-[15N,1H]-TROSY
1723D (H)C(CC)-TOCSY-(CA)-[15N,1H]-TROSY
1823D H(CCCO)-TOCSY
1932D [1H,13C]-CT-HSQC
11014D 15N,15N-separated HMQC-NOESY-TROSY
11143D 15N,13C-separated HMQC-NOESY-TROSY
11243D 13C,13C-separated HMQC-NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] KpOmpA transmembrane domain, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3] KpOmpA transmembrane domain, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-15N;10%-13C] KpOmpA transmembrane domain, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3] KpOmpA transmembrane domain, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKpOmpA transmembrane domain[U-13C; U-15N; U-2H]1
1 mMKpOmpA transmembrane domain[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]2
1 mMKpOmpA transmembrane domain[U-15N;10%-13C]3
1 mMKpOmpA transmembrane domain[U-13C; U-15N; U-2H]/[L,V,I(delta1)-13CH3]4
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004
Bruker AvanceBrukerAVANCE5005

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewv5.2.2Johnson, One Moon Scientificdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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