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- PDB-6oqh: Solution NMR structure of a quiet outer membrane protein G Nanopo... -

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Basic information

Entry
Database: PDB / ID: 6oqh
TitleSolution NMR structure of a quiet outer membrane protein G Nanopore (OmpG mutant: Delta-L6-D215)
ComponentsOuter membrane protein G
KeywordsMEMBRANE PROTEIN / Outer membrane protein b-barrel Solution NMR
Function / homology
Function and homology information


carbohydrate transmembrane transport / oligosaccharide transporting porin activity / maltose transporting porin activity / porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Outer membrane porin G / Outer membrane protein G (OmpG) / :
Similarity search - Domain/homology
Outer membrane porin G
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSanganna Gari, R.R. / Seelheim, P. / Liang, B. / Tamm, L.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM051329 United States
CitationJournal: ACS Sens / Year: 2019
Title: Quiet Outer Membrane Protein G (OmpG) Nanopore for Biosensing.
Authors: Sanganna Gari, R.R. / Seelheim, P. / Liang, B. / Tamm, L.K.
History
DepositionApr 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein G


Theoretical massNumber of molelcules
Total (without water)31,5021
Polymers31,5021
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer membrane protein G


Mass: 31502.029 Da / Num. of mol.: 1 / Mutation: L6 deletion, D215 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: ompG, b1319, JW1312 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P76045

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D 15N-1H-1H NOESY-TROSY
161isotropic13D 15N-1H-15N HSQC-NOESY-HSQC
171isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: micelle
Contents: 1 mM [U-13C; U-15N; U-2H] OmpG delta-L6-D215 mutant, 200 mM DPC, 25 mM Bis-Tris, 50 mM sodium chloride, 0.05 % w/v sodium azide, 90% H2O/10% D2O
Label: DCN_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMOmpG delta-L6-D215 mutant[U-13C; U-15N; U-2H]1
200 mMDPCnatural abundance1
25 mMBis-Trisnatural abundance1
50 mMsodium chloridenatural abundance1
0.05 % w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 6.3 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3Goddard and Knellerchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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