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- PDB-2n6l: Solution NMR structure of Outer Membrane Protein G from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 2n6l
TitleSolution NMR structure of Outer Membrane Protein G from Pseudomonas aeruginosa
ComponentsOuter membrane protein OprG
KeywordsMEMBRANE PROTEIN
Function / homologyOuter membrane protein, OmpW / OmpW family / Enterobacterial virulence outer membrane protein signature 2. / host outer membrane / Virulence-related outer membrane protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / transmembrane transport / Outer membrane protein OprG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKucharska, I. / Seelheim, P. / Edrington, T.C. / Liang, B. / Tamm, L.K.
CitationJournal: Structure / Year: 2015
Title: OprG Harnesses the Dynamics of its Extracellular Loops to Transport Small Amino Acids across the Outer Membrane of Pseudomonas aeruginosa.
Authors: Kucharska, I. / Seelheim, P. / Edrington, T. / Liang, B. / Tamm, L.K.
History
DepositionAug 25, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein OprG


Theoretical massNumber of molelcules
Total (without water)23,7151
Polymers23,7151
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer membrane protein OprG


Mass: 23714.643 Da / Num. of mol.: 1 / Fragment: UNP residues 27-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: 879793, oprG, PA4067 / Plasmid: Pet30a+ / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWW1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H 15N TROSY
1213D HNCO
1313D HNCA
1413D HNCB
1513D HNCA(CO)
1612D 1H 15N TROSY
1713D 15N 1H 1H NOESY TROSY
1814D 15N 1H 15N HSQC NOESY HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-13C; U-15N; U-2H] protein, 25 mM sodium phosphate, 50 mM potassium chloride, 0.05 % sodium azide, 0.9 % 1,2-dihexanoyl-sn-glycero-3-phosphocholine, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N; U-2H] protein, 25 mM sodium phosphate, 50 mM potassium chloride, 0.05 % sodium azide, 0.9 % 1,2-dihexanoyl-sn-glycero-3-phosphocholine, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein-1[U-13C; U-15N; U-2H]1
25 mMsodium phosphate-21
50 mMpotassium chloride-31
0.05 %sodium azide-41
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-51
1 mMprotein-6[U-13C; U-15N; U-2H]2
25 mMsodium phosphate-72
50 mMpotassium chloride-82
0.05 %sodium azide-92
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-102
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 318 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
SparkyT. D. Goddard and D. G. Knellerdata analysis
CNS1.2Brunger, A.T. et al.structure solution
TopSpin2.1.6Brukercollection
NMRPipeF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
CNS1.2Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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