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- PDB-8rjx: Solution structure of osmoregulator OsmY from E. coli. -

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Basic information

Entry
Database: PDB / ID: 8rjx
TitleSolution structure of osmoregulator OsmY from E. coli.
ComponentsOsmotically-inducible protein Y
KeywordsTRANSPORT PROTEIN / osmoregulatory protein bacterial protein
Function / homology
Function and homology information


hyperosmotic response / response to osmotic stress / chaperone-mediated protein folding / outer membrane-bounded periplasmic space
Similarity search - Function
Transport-associated and nodulation domain, bacteria / bacterial OsmY and nodulation domain / BON domain profile. / BON domain / BON domain
Similarity search - Domain/homology
Osmotically-inducible protein Y
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsIyer, A. / Luo, Y. / le Paige, U.B.A. / van Ingen, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2024
Title: The Structure and Function of the Bacterial Osmotically Inducible Protein Y.
Authors: Iyer, A. / Frallicciardi, J. / le Paige, U.B.A. / Narasimhan, S. / Luo, Y. / Sieiro, P.A. / Syga, L. / van den Brekel, F. / Tran, B.M. / Tjioe, R. / Schuurman-Wolters, G. / Stuart, M.C.A. / ...Authors: Iyer, A. / Frallicciardi, J. / le Paige, U.B.A. / Narasimhan, S. / Luo, Y. / Sieiro, P.A. / Syga, L. / van den Brekel, F. / Tran, B.M. / Tjioe, R. / Schuurman-Wolters, G. / Stuart, M.C.A. / Baldus, M. / van Ingen, H. / Poolman, B.
History
DepositionDec 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Osmotically-inducible protein Y


Theoretical massNumber of molelcules
Total (without water)19,1871
Polymers19,1871
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)20 / 200structures with the lowest energy
RepresentativeModel #1closest to mean

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Components

#1: Protein Osmotically-inducible protein Y


Mass: 19187.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: osmY, b4376, JW4338 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFH8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-15N NOESY
131isotropic23D HNCA
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 0.73 mM [U-100% 13C; U-100% 15N] Osmotically-inducible protein Y (OsmY), 50 mM NA KPi, 100 mM NA NaCl, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.73 mMOsmotically-inducible protein Y (OsmY)[U-100% 13C; U-100% 15N]1
50 mMKPiNA1
100 mMNaClNA1
Sample conditionsIonic strength: 100 Not defined / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYLee, W.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 3 / Details: explicit solvent
NMR representativeSelection criteria: closest to mean
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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