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- PDB-2n6p: Solution NMR structure of Outer Membrane Protein G P92A mutant fr... -

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Basic information

Entry
Database: PDB / ID: 2n6p
TitleSolution NMR structure of Outer Membrane Protein G P92A mutant from Pseudomonas aeruginosa
ComponentsOuter membrane protein OprG
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


host outer membrane / outer membrane / transmembrane transport / membrane
Similarity search - Function
Outer membrane protein, OmpW / OmpW family / Virulence-related outer membrane protein / Enterobacterial virulence outer membrane protein signature 2. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel
Similarity search - Domain/homology
Outer membrane protein OprG
Similarity search - Component
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 27, 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 / 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 / _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)23,6891
Polymers23,6891
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: 23688.605 Da / Num. of mol.: 1 / Fragment: UNP residues 27-232 / Mutation: P92A
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)
1622D 1H 15N TROSY
1732D 1H 15N TROSY
1842D 1H 15N TROSY
1952D 1H 15N TROSY
11062D 1H 15N TROSY
11172D 1H 15N TROSY
11213D 15N 1H 1H NOESY TROSY
11314D 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
31 mM 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
41 mM 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
51 mM 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
61 mM 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
71 mM [U-15N]-Leu 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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-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 mMentity-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
1 mMentity-113
25 mMsodium phosphate-123
50 mMpotassium chloride-133
0.05 %sodium azide-143
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-153
1 mMentity-164
25 mMsodium phosphate-174
50 mMpotassium chloride-184
0.05 %sodium azide-194
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-204
1 mMentity-215
25 mMsodium phosphate-225
50 mMpotassium chloride-235
0.05 %sodium azide-245
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-255
1 mMentity-266
25 mMsodium phosphate-276
50 mMpotassium chloride-286
0.05 %sodium azide-296
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-306
1 mMentity-31[U-15N]-Leu7
25 mMsodium phosphate-327
50 mMpotassium chloride-337
0.05 %sodium azide-347
0.9 %1,2-dihexanoyl-sn-glycero-3-phosphocholine-357
Sample conditionspH: 6 / Pressure: ambient / Temperature: 318 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
TALOSTalos+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxrediction of protein backbone torsion angles from nmr chemical shifts
SparkyT. D. Goddard and D. G. Knellernmr assignments
CNS1.2Brunger, A.T. et al.structure solution
Bruker_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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