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- PDB-2ge4: High-resolution solution structure of outer membrane protein A tr... -

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Basic information

Entry
Database: PDB / ID: 2ge4
TitleHigh-resolution solution structure of outer membrane protein A transmembrane domain
ComponentsOuter membrane protein A
KeywordsMEMBRANE PROTEIN / beta barrel
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 / simulated annealing
AuthorsCierpicki, T. / Liang, B. / Tamm, L.K. / Bushweller, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Increasing the accuracy of solution NMR structures of membrane proteins by application of residual dipolar couplings. High-resolution structure of outer membrane protein A.
Authors: Cierpicki, T. / Liang, B. / Tamm, L.K. / Bushweller, J.H.
History
DepositionMar 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 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)19,1921
Polymers19,1921
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 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 19192.178 Da / Num. of mol.: 1 / Fragment: transmembrane domain / Mutation: W15F, W57F, W102F, W143F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompA, con, tolG, tut / Production host: Escherichia coli (E. coli) / References: UniProt: P0A910

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO based experiment for measurement 1JHN couplings
121HNCO based experiment for measurement 1JNC' couplings
131HNCO based experiment for measurement 1JC'Ca couplings
NMR detailsText: distance restraints, hydrogen bonds and dihedral angles were the same as for previous NMR structure (PDB code 1g90)

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Sample preparation

DetailsContents: 1mM OmpA U-2H,13C,15N; 500mM DPC; 10mM phosphate buffer; pH 6.3; 50mM NaCl
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 6.3 / Pressure: ambient / Temperature: 223 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Version: 1.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: refinement using RDCs
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 10

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