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- PDB-7uo6: NMR structure of Pheromone-binding protein 2 in Ostrinia furnacalis -

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Basic information

Entry
Database: PDB / ID: 7uo6
TitleNMR structure of Pheromone-binding protein 2 in Ostrinia furnacalis
ComponentsPheromone binding protein 2
KeywordsSIGNALING PROTEIN / pheromone binding
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 2
Function and homology information
Biological speciesOstrinia furnacalis (Asian corn borer)
MethodSOLUTION NMR / simulated annealing
AuthorsAyyappan, S. / Mohanty, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1807722 United States
National Science Foundation (NSF, United States)DBI-1726397 United States
National Science Foundation (NSF, United States)DMR-1644779 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Ostrinia furnacalis PBP2 solution NMR structure: Insight into ligand binding and release mechanisms.
Authors: Dahal, S.R. / Lewellen, J.L. / Ayyappan, S. / Chaudhary, B.P. / Nukala, V. / Mohanty, S.
History
DepositionApr 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pheromone binding protein 2


Theoretical massNumber of molelcules
Total (without water)16,1231
Polymers16,1231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pheromone binding protein 2


Mass: 16122.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Gene: PBP2, OfurPBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: E7CCA0
Has protein modificationY

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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
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D HN(CA)CB
161isotropic13D HNCA

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Sample preparation

DetailsType: solution
Contents: 400 uM [U-13C; U-15N] Pheromone-binding protein 2, 90% H2O/10% D2O
Label: U-13C; U-15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 400 uM / Component: Pheromone-binding protein 2 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: sample_conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRFAM-SPARKYMarkley JL.chemical shift assignment
NMRFAM-SPARKYMarkley JL.peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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