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- PDB-8qwq: Magic-angle spinning NMR Structure of Opa60 in Lipid Bilayers -

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Basic information

Entry
Database: PDB / ID: 8qwq
TitleMagic-angle spinning NMR Structure of Opa60 in Lipid Bilayers
ComponentsOpacity protein opA60 (Fragment)
KeywordsCELL ADHESION / STRUCTURE FROM CYANA 3.98.15 / BETA BARREL / BACTERIAL OUTER MEMBRANE
Function / homologyPorin, opacity type / Opacity family porin protein / Outer membrane autotransporter barrel / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / porin activity / Cell surface interactions at the vascular wall / cell outer membrane / Opacity protein opA60
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsForster, M.C. / Andreas, L.B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)AN1316 Germany
CitationJournal: J Struct Biol X / Year: 2024
Title: Magic-angle spinning NMR structure of Opa60 in lipid bilayers.
Authors: Forster, M.C. / Tekwani Movellan, K. / Najbauer, E.E. / Becker, S. / Andreas, L.B.
History
DepositionOct 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Opacity protein opA60 (Fragment)


Theoretical massNumber of molelcules
Total (without water)28,7731
Polymers28,7731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 2000target function
RepresentativeModel #1target function

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Components

#1: Protein Opacity protein opA60 (Fragment)


Mass: 28772.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: opaH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04884

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
1121isotropic1(H)NH
111isotropic1(H)CANH
121isotropic1(H)(CO)CA(CO)NH
131isotropic2(H)(CA)CB(CA)NH
141isotropic2(H)(CA)CB(CA)(CO)NH
151isotropic1(H)CONH
161isotropic1(H)CO(CA)NH
171isotropic1(H)N(CA)(CO)NH
181isotropic1HN(H)(H)NH
192isotropic3(H)CANH
1102isotropic3(H)NCAHA
1112isotropic3HC(H)(H)CH

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
membrane120 mM NA sodium phosphate, 100 mM NA sodium chloride, 20 mM NA magnesium chloride, 33 % w/w NA dimyristoyl-sn-glycero-3-phosphocholine, 67 % w/w [U-99% 13C; U-99% 15N; U-98% 2H] protein, waterLipid bilayer reconstitution2H13C15N_samplewater
membrane220 mM NA sodium phosphate, 100 mM NA sodium chloride, 20 mM NA magnesium chloride, 33 % w/w Acyl chain deuterated (d54) dimyristoyl-sn-glycero-3-phosphocholine, 67 % w/w [U-99% 13C; U-99% 15N; U-98% 2H] protein, waterLipid bilayer reconstitution1H13C15N_samplewater
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphateNA1
100 mMsodium chlorideNA1
20 mMmagnesium chlorideNA1
33 % w/wdimyristoyl-sn-glycero-3-phosphocholineNA1
67 % w/wprotein[U-99% 13C; U-99% 15N; U-98% 2H]1
20 mMsodium phosphateNA2
100 mMsodium chlorideNA2
20 mMmagnesium chlorideNA2
33 % w/wdimyristoyl-sn-glycero-3-phosphocholineAcyl chain deuterated (d54)2
67 % w/wprotein[U-99% 13C; U-99% 15N; U-98% 2H]2
Sample conditionsIonic strength: 140 mM / Label: conditions / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD80011.3 mm HCN probe
Bruker AVANCE III HDBrukerAVANCE III HD60021.3 mm HCN probe
Bruker AVANCE III HDBrukerAVANCE III HD95030.7 mm HCND probe

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYLee W, Tonelli M, Markley JLdata analysis
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 10

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