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- PDB-6qwr: Solid-state NMR structure of outer membrane protein AlkL in DMPC ... -

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Basic information

Entry
Database: PDB / ID: 6qwr
TitleSolid-state NMR structure of outer membrane protein AlkL in DMPC lipid bilayers
ComponentsOuter membrane protein AlkL
KeywordsMEMBRANE PROTEIN / Outer membrane protein / Beta Barrel / Porin / Transporter
Function / homologyOuter membrane protein, OmpW / OmpW family / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / cell outer membrane / Outer membrane protein AlkL
Function and homology information
Biological speciesPseudomonas oleovorans (bacteria)
MethodSOLID-STATE NMR / simulated annealing
AuthorsSchubeis, T. / Andreas, L.B. / Pintacuda, G.
Funding support France, Germany, 2items
OrganizationGrant numberCountry
European Research Council648974 France
German Research FoundationAN1316/1-1 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: A beta-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL.
Authors: Schubeis, T. / Le Marchand, T. / Daday, C. / Kopec, W. / Tekwani Movellan, K. / Stanek, J. / Schwarzer, T.S. / Castiglione, K. / de Groot, B.L. / Pintacuda, G. / Andreas, L.B.
History
DepositionMar 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Jun 19, 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 AlkL


Theoretical massNumber of molelcules
Total (without water)24,0881
Polymers24,0881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14760 Å2
MethodPISA
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 AlkL


Mass: 24087.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas oleovorans (bacteria) / Gene: alkL / Production host: Escherichia coli (E. coli) / References: UniProt: Q00595

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D hCANH
121isotropic23D hCONH
131isotropic23D hcoCAcoNH
141isotropic23D hcaCBcaNH
151isotropic23D hcaCBcacoNH
161isotropic23D hNCAHa
171isotropic23D hNcoCAHa
181isotropic23D hCOCAHa
191isotropic23D hCOnCAHa
1101isotropic23D (H)CCH-TOCSY
1151isotropic23D hNHH BASS-SD
1161isotropic23D hNNH BASS-SD
1171isotropic23D (H)CCH BASS-SD
1181isotropic23D hNHH RFDR
1191isotropic23D hCHH RFDR
1112isotropic33D hCANH
1122isotropic33D hCONH
1132isotropic33D hcoCAcoNH
1142isotropic33D hCOcaNH
1202isotropic34D HNNH RFDR

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
liposome10.5 w/w [U-13C; U-15N] Outer membrane protein AlkL, WaterDMPC L/P ratio 0.5 (w/w)CNWater
liposome20.5 w/w [U-13C; U-15N; U-2H] Outer membrane protein AlkL, WaterDMPC L/P ratio 0.5 (w/w)DCNWater
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 w/wOuter membrane protein AlkL[U-13C; U-15N]1
0.5 w/wOuter membrane protein AlkL[U-13C; U-15N; U-2H]2
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III100020.7 mm Rotor 111 kHz MAS
Bruker AVANCE IIIBrukerAVANCE III80031.3 mm Rotor 60 kHz MAS

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
CcpNmr AnalysisCCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
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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