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- PDB-1tuj: Solution structure of the honey bee general odorant binding prote... -

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Basic information

Entry
Database: PDB / ID: 1tuj
TitleSolution structure of the honey bee general odorant binding protein ASP2 in complex with trimethylsilyl-d4 propionate
Componentsodorant binding protein ASP2
KeywordsTRANSPORT PROTEIN / ALPHA HELIX / COMPLEX / TSP / ODORANT-BINDING PROTEIN
Function / homology
Function and homology information


odorant binding / extracellular region
Similarity search - Function
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
3-TRIMETHYLSILYL-PROPIONATE-2,2,3,3,-D4 / Odorant binding protein ASP2
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodSOLUTION NMR / automatic NOE assignment using ARIA, CNS
AuthorsLescop, E. / Briand, L. / Pernollet, J.-C. / Guittet, E.
Citation
Journal: To be Published
Title: Solution structure of the honey bee general odorant binding protein ASP2 in complex with trimethylsilyl-d4 propionate
Authors: Lescop, E. / Briand, L. / Pernollet, J.-C. / Guittet, E.
#1: Journal: J.Biomol.NMR / Year: 2001
Title: 1H, 13C and 15N chemical shift assignment of the honeybee odorant-binding protein ASP2
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: odorant binding protein ASP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8632
Polymers13,7141
Non-polymers1491
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 100structures with the lowest energy
RepresentativeModel #1see article

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Components

#1: Protein odorant binding protein ASP2


Mass: 13713.742 Da / Num. of mol.: 1 / Fragment: residues 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: ASP2 / Plasmid: pNatASP2 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q9U9J5
#2: Chemical ChemComp-TSD / 3-TRIMETHYLSILYL-PROPIONATE-2,2,3,3,-D4


Mass: 149.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9O2Si
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2223D 13C-separated NOESY
1332D NOESY
141HNHA
NMR detailsText: The structure was determined using classical triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM ASP2 U-15N; 30mM TSP; 0.1mM sodium azide; 100mM sodium phosphate buffer90% H2O/10% D2O
21mM ASP2 U-15N,U-13C; 30mM TSP; 0.1mM sodium azide; 100mM sodium phosphate buffer100% D2O
31mM ASP2 unlabelled; 30mM TSP; 0.1mM sodium azide; 100mM sodium phosphate buffer100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16ambient 308 K
28ambient 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerManufacturer: Bruker / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe2.1Delaglioprocessing
NMRView5.0.4Johnsondata analysis
CNS1.1Brungerstructure solution
ARIA1.2Linge, Nilgesstructure solution
ARIA1.2Linge, Nilgesrefinement
RefinementMethod: automatic NOE assignment using ARIA, CNS / Software ordinal: 1
Details: the structures are based on a total of 2471 restraints, 2348 are NOE-derived distance constraints, 86 dihedral angle restraints, 37 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: see article
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 17

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