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- PDB-6um9: Gypsy Moth Pheromone-binding protein 1 (LdisPBP1) NMR Structure a... -

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Basic information

Entry
Database: PDB / ID: 6um9
TitleGypsy Moth Pheromone-binding protein 1 (LdisPBP1) NMR Structure at pH 4.5
ComponentsPheromone binding protein 1
KeywordsLIPID BINDING PROTEIN
Function / homologyOdorant/pheromone binding protein, Lepidoptera / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / Pheromone binding protein 1
Function and homology information
Biological speciesLymantria dispar (gypsy moth)
MethodSOLUTION NMR / STAP
AuthorsTerrado, M. / Plettner, E.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)06088 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)05053 Canada
CitationJournal: Biochemistry / Year: 2020
Title: Ligand- and pH-Induced Structural Transition of Gypsy Moth Lymantria dispar Pheromone-Binding Protein 1 (LdisPBP1).
Authors: Terrado, M. / Okon, M. / McIntosh, L.P. / Plettner, E.
History
DepositionOct 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pheromone binding protein 1


Theoretical massNumber of molelcules
Total (without water)16,1661
Polymers16,1661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1target function

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Components

#1: Protein Pheromone binding protein 1


Mass: 16165.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymantria dispar (gypsy moth) / Gene: PBP1 / Plasmid: pET 30 Xa/LIC / Production host: Escherichia coli (E. coli) / References: UniProt: O16105

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CO)CA
171isotropic13D C(CO)NH
181isotropic13D HBHA(CO)NH
191isotropic23D 1H-13C NOESY
1101isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.2 M [U-99% 13C; U-99% 15N] LdisPBP1, 50 mM sodium acetate, 1 mM EDTA, 0.05 % w/v sodium azide, 95% H2O/5% D2O
Details: in 50 mM sodium acetate buffer pH 4.5, 1 mM EDTA, 0.05% NaN3
Label: 13C,15N LdisPBP1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 MLdisPBP1[U-99% 13C; U-99% 15N]1
50 mMsodium acetatenatural abundance1
1 mMEDTAnatural abundance1
0.05 % w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 0 M / Label: buffer / pH: 4.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
NMReRyu H, Lim GT, Sung BH, Lee Jrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: STAP / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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