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- PDB-1qwv: Solution structure of Antheraea polyphemus pheromone binding prot... -

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Basic information

Entry
Database: PDB / ID: 1qwv
TitleSolution structure of Antheraea polyphemus pheromone binding protein (ApolPBP)
ComponentsPheromone-binding protein
KeywordsTRANSPORT PROTEIN / pheromone binding protein / Antheraea polyphemus / PBP / ApolPBP / hexahelical fold / PBP fold
Function / homology
Function and homology information


response to pheromone / pheromone binding
Similarity search - Function
Odorant/pheromone binding protein, Lepidoptera / Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Pheromone-binding protein
Similarity search - Component
Biological speciesAntheraea polyphemus (polyphemus moth)
MethodSOLUTION NMR / torsion angle dynamics simulated annealing, thin layer water refinement
AuthorsMohanty, S. / Zubkov, S. / Gronenborn, A.M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Solution NMR Structure of Antheraea polyphemus PBP Provides New Insight into Pheromone Recognition by Pheromone-binding Proteins
Authors: Mohanty, S. / Zubkov, S. / Gronenborn, A.M.
History
DepositionSep 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pheromone-binding protein


Theoretical massNumber of molelcules
Total (without water)15,8021
Polymers15,8021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #3closest to the average

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Components

#1: Protein Pheromone-binding protein / PBP


Mass: 15802.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Antheraea polyphemus (polyphemus moth) / Plasmid: pHN1+ / Production host: Escherichia coli (E. coli) / Strain (production host): XA-90 / References: UniProt: P20797

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: mixing time 110ms for 13C separated NOESY, 120ms for 15N separated NOESY

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Sample preparation

DetailsContents: 1mM ApolPBP U-15N,13C; 50mM phosphate buffer; 1mM EDTA; 0.1% NaN3; 95% H2O; 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 50mM phosphate / pH: 6.33 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfizer J., Bax A.processing
NMRView5.0.4Johnson B.A., Blevins R.A.data analysis
CYANA1.0.6Guntert P., Mumenthaler C., Wuthrich K.structure solution
ARIA1.2Linge J.P., Habeck M., Rieping W., Nilges M.refinement
RefinementMethod: torsion angle dynamics simulated annealing, thin layer water refinement
Software ordinal: 1
Details: 2501 NOE-derived distance constraints, 243 dihedral angle restraints, 120 distance restraints from hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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