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- PDB-1g90: NMR Solution Structure of Outer Membrane Protein A Transmembrane ... -

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Basic information

Entry
Database: PDB / ID: 1g90
TitleNMR Solution Structure of Outer Membrane Protein A Transmembrane Domain: 10 conformers
ComponentsOUTER MEMBRANE PROTEIN A
KeywordsMEMBRANE PROTEIN / BETA BARREL / INTEGRAL MEMBRANE PROTEIN
Function / homology
Function and homology information


outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell / DNA damage response / identical protein binding / 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 ...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 speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsArora, A. / Abildgaard, F. / Bushweller, J.H. / Tamm, L.K.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Structure of outer membrane protein A transmembrane domain by NMR spectroscopy
Authors: Arora, A. / Abildgaard, F. / Bushweller, J.H. / Tamm, L.K.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 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: OUTER MEMBRANE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)19,0611
Polymers19,0611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein OUTER MEMBRANE PROTEIN A / OUTER MEMBRANE PROTEIN II* / OMPA PROTEIN


Mass: 19060.982 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN, RESIDUES 1-176 / Mutation: W15F, W57F, W102F, W103F.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OMPA / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A910

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY-TROSY
1213D-HNCA-TROSY
1313D-HN(CA)CB-TROSY
1413D-HNCO-TROSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1mM OmpA(0-176) U-15N,13C,2H; 600 mM D38-DPC; 10 mM phosphate buffer; pH 6.3; 50 mM NaCl
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.05 / pH: 6.3 / Pressure: ambient / Temperature: 323 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
OPAL2.6Luginbuhlrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 349 restraints, 91 are NOE-derived distance constraints, 142 dihedral angle restraints,116 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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