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- PDB-5mwv: Solid-state NMR Structure of outer membrane protein G in lipid bi... -

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Basic information

Entry
Database: PDB / ID: 5mwv
TitleSolid-state NMR Structure of outer membrane protein G in lipid bilayers
ComponentsOuter membrane protein G
KeywordsMEMBRANE PROTEIN / porin beta-barrel membrane lipid
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 K12 (bacteria)
MethodSOLID-STATE NMR / molecular dynamics
AuthorsRetel, J.S. / Nieuwkoop, A.J. / Hiller, M. / Higman, V.A. / Barbet-Massin, E. / Stanek, J. / Andreas, L.B. / Franks, W.T. / van Rossum, B.-J. / Vinothkumar, K.R. ...Retel, J.S. / Nieuwkoop, A.J. / Hiller, M. / Higman, V.A. / Barbet-Massin, E. / Stanek, J. / Andreas, L.B. / Franks, W.T. / van Rossum, B.-J. / Vinothkumar, K.R. / Handel, L. / de Palma, G.G. / Bardiaux, B. / Pintacuda, G. / Emsley, L. / Kuelbrandt, W. / Oschkinat, H.
Funding support Germany, 4items
OrganizationGrant numberCountry
European UnionBioNMR / 261863 Germany
European UnioniNext / GA 653706
German Research FoundationSFB 740 Germany
German Research FoundationOS106/9 Germany
CitationJournal: Nat Commun / Year: 2017
Title: Structure of outer membrane protein G in lipid bilayers.
Authors: Retel, J.S. / Nieuwkoop, A.J. / Hiller, M. / Higman, V.A. / Barbet-Massin, E. / Stanek, J. / Andreas, L.B. / Franks, W.T. / van Rossum, B.J. / Vinothkumar, K.R. / Handel, L. / de Palma, G.G. ...Authors: Retel, J.S. / Nieuwkoop, A.J. / Hiller, M. / Higman, V.A. / Barbet-Massin, E. / Stanek, J. / Andreas, L.B. / Franks, W.T. / van Rossum, B.J. / Vinothkumar, K.R. / Handel, L. / de Palma, G.G. / Bardiaux, B. / Pintacuda, G. / Emsley, L. / Kuhlbrandt, W. / Oschkinat, H.
History
DepositionJan 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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)32,9371
Polymers32,9371
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22310 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Outer membrane protein G /


Mass: 32936.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: ompG, b1319, JW1312 / Production host: Escherichia coli (E. coli) / References: UniProt: P76045

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D (H)N(HH)NH RFDR 2ms
121isotropic23D (H)NHH RFDR 2ms
232isotropic12D 13C-13C DARR 200ms
242isotropic12D 13C-13C DARR 400ms
253isotropic12D 13C-13C DARR 200ms
263isotropic12D 13C-13C DARR 400ms
284isotropic12D 13C-13C DARR 150ms
274isotropic12D 13C-13C DARR 400ms
295isotropic12D 13C-13C DARR 150ms
2105isotropic12D 13C-13C DARR 400ms
2116isotropic12D 13C-13C DARR 150ms
2126isotropic12D 13C-13C DARR 400ms
2137isotropic12D 13C-13C DARR 500ms
1141isotropic23D (H)CANH
3158isotropic33D (H)CANH
3168isotropic33D (HCO)CA(CO)NH
3178isotropic33D (HCA)CB(CA)NH
3188isotropic33D (HCA)CBCA(CO)NH
3198isotropic33D (H)CONH
3208isotropic33D (H)CO(CA)NH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid10.66 w/w [U-13C; U-15N; U-2H] backexchanged 1H Outer Membrane Protein G, 0.33 w/w lipids, MES BufferFully deuterated. Subsequently the exchangeable sites were back-exchanged with 100% 1H.deuterated-back-exchanged-OmpGMES Buffer
solid80.66 w/w [U-13C; U-15N; U-2H] backexchanged 1H Outer Membrane Protein G, HEPES BufferFully deuterated. Subsequently the exchangeable sites were back-exchanged with 70% 1H.deuterated-70-back-exchanged-OmpGHEPES Buffer
solid20.66 w/w [U-15N; U-1H] Outer Membrane Protein G, 0.33 w/w lipids, HEPES BufferUniformly 1H and 15N labeled. 13C labeling as obtained by using 1,3-labeled glycerol as the sole carbon source during protein expression1,3-glycerol-OmpGHEPES Buffer
solid30.66 w/w [U-15N; U-1H] Outer Membrane Protein G, 0.33 w/w lipids, HEPES BufferUniformly 1H and 15N labeled. 13C labeling as obtained by using 2-labeled glycerol as the sole carbon source during protein expression2-glycerol-OmpGHEPES Buffer
solid40.66 w/w [U-15N; U-1H] Outer Membrane Protein G, 0.33 w/w lipids, HEPES BufferUniformly 1H and 15N labeled. The residues T,E,M,P,Q,A,N,S,G are 13C labeled as obtained by using 1,3-labeled glycerol as the sole carbon source during protein expression. Other amino acids are not 13C labeled.1,3-TEMPQANDSG-OmpGHEPES Buffer
solid50.66 w/w [U-15N; U-1H] Outer Membrane Protein G, 0.33 w/w lipids, HEPES BufferUniformly 1H and 15N labeled. The residues T,E,M,P,Q,A,N,S,G are 13C labeled as obtained by using 2-labeled glycerol as the sole carbon source during protein expression. Other amino acids are not 13C labeled.2-TEMPQANDSG-OmpGHEPES Buffer
solid60.66 w/w [U-15N; U-1H] Outer Membrane Protein G, 0.33 w/w na lipids, HEPES BufferUniformly 1H and 15N labeled. The residues S,H,L,Y,G,W,A,F,V are 13C labeled as obtained by using 2-labeled glycerol as the sole carbon source during protein expression. Other amino acids are not 13C labeled.2-SHLYGWAFV-OmpGHEPES Buffer
solid70.66 w/w [U-15N; U-1H] Outer Membrane Protein G, 0.33 w/w lipids, HEPES BufferUniformly 1H and 15N labeled. The residues G and A are 13C labeled. F and Y are 13C labeled on the CA and CB.GAF23Y23-OmpGHEPES Buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.66 w/wOuter Membrane Protein G[U-13C; U-15N; U-2H] backexchanged 1H1
0.33 w/wlipidsnatural abundance1
0.66 w/wOuter Membrane Protein G[U-13C; U-15N; U-2H] backexchanged 1H8
0.66 w/wOuter Membrane Protein G[U-15N; U-1H]2
0.33 w/wlipidsnatural abundance2
0.66 w/wOuter Membrane Protein G[U-15N; U-1H]3
0.33 w/wlipidsnatural abundance3
0.66 w/wOuter Membrane Protein G[U-15N; U-1H]4
0.33 w/wlipidsnatural abundance4
0.66 w/wOuter Membrane Protein G[U-15N; U-1H]5
0.33 w/wlipidsnatural abundance5
0.66 w/wOuter Membrane Protein G[U-15N; U-1H]6
0.33 w/wlipidsna6
0.66 w/wOuter Membrane Protein G[U-15N; U-1H]7
0.33 w/wlipidsnatural abundance7
Sample conditions

Ionic strength: 50 mM NaCl mM / Pressure: 1 atm / Temperature: 280 K

Conditions-IDDetailsLabelpHTemperature err
1There is a large error on the sample temperature due to fast MAS spinning (60 kHz).proton-detection-distances6.3 20
3There is a large error on the sample temperature due to fast MAS spinning (60kHz).proton-detection-initial-assignment6.8 20
2Condition at experiments at lower MAS rates (13 kHz).carbon-detection6.8

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE9001Berlin
Bruker AVANCEBrukerAVANCE10002Lyon
Bruker AVANCEBrukerAVANCE8003Lyon

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
ARIA1.21Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNpeak picking
TALOSTALOS+Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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