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- PDB-6nbn: Structure of Aedes aegypti OBP22 in the complex with arachidonic acid -

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Basic information

Entry
Database: PDB / ID: 6nbn
TitleStructure of Aedes aegypti OBP22 in the complex with arachidonic acid
ComponentsAAEL005772-PA
KeywordsTRANSPORT PROTEIN / Odorant binding protein Chemo-sensory signaling Lipid binding
Function / homology
Function and homology information


odorant binding / sensory perception of smell / lipid binding / extracellular space
Similarity search - Function
Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily
Similarity search - Domain/homology
ARACHIDONIC ACID / Odorant-binding protein 22
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodSOLUTION NMR / simulated annealing
AuthorsJones, D.N. / Wang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI121253 United States
CitationJournal: Sci Rep / Year: 2020
Title: Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail.
Authors: Wang, J. / Murphy, E.J. / Nix, J.C. / Jones, D.N.M.
History
DepositionDec 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 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
Revision 1.4Oct 23, 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: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7052
Polymers14,4001
Non-polymers3041
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Fluorescence competition binding assays and NMR titrations support binding of lipid to protein
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 50NOE violation energy
RepresentativeModel #1medoid

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Components

#1: Protein AAEL005772-PA / Odorant binding protein


Mass: 14400.319 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Tissue: Antennal cDNA / Gene: 5567053, AAEL005772 / Plasmid: PET1a / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q1HRL7
#2: Chemical ChemComp-ACD / ARACHIDONIC ACID


Mass: 304.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32O2
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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
2172isotropic12D (HB)CB(CGCD)HD
141isotropic23D HN(CA)CB
151isotropic23D CBCA(CO)NH
161isotropic23D C(CO)NH
1101isotropic23D HBHA(CO)NH
191isotropic23D HNCO
181isotropic23D (HACA)CO(CA)NH
171isotropic13D 13C/15N- NOESY-HSQC
1131isotropic13D 13C/15N-NOESY-HSQC (AROMATIC)
2122isotropic13D 12C-filtered-13C/15N-editedNOESY-HSQC
2112isotropic12D 12C-filtered-1H-1H-NOESY
2152isotropic12D 12C-filterd-1H-1H-TOCSY
2142isotropic13D HAHB
2162isotropic12D (HB)CB(CGCDCE)HE
2182isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1650 uM [U-13C; U-15N] OBP22, 650 uM ARACHIDONIC ACID, 20 mM sodium phosphate, 90% H2O/10% D2O15N/C13 H2O90% H2O/10% D2O
solution2670 uM [U-95% 13C; U-98% 15N] Aedes aegypti odorant binding protein 22, 670 uM ARACHIDONIC ACID, 20 mM sodium phosphate, 99% D2O/1 % H2O15N/C13 D2O99% D2O/1 % H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
650 uMOBP22[U-13C; U-15N]1
650 uMARACHIDONIC ACIDnatural abundance1
20 mMsodium phosphatenatural abundance1
670 uMAedes aegypti odorant binding protein 22[U-95% 13C; U-98% 15N]2
670 uMARACHIDONIC ACIDnatural abundance2
20 mMsodium phosphatenatural abundance2
Sample conditions

Ionic strength: 20 mM / Ionic strength err: 0.2 / Pressure: 820 mbar / Temperature: 298 K / Temperature err: 1

Conditions-IDLabelpHPH errPressure err
1H2O_Sample6.50.110
2D2O_Sample6.1 pD0.055

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian DD2VarianDD29001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
Analysis2.4.2CCPNchemical shift assignment
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Analysis2.4.2CCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
Details: Structure were determined using the unambiguous assignment protocol in Aria2 using a final total of 2381 restraint of which 1998 were NOE based
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: NOE violation energy / Conformers calculated total number: 50 / Conformers submitted total number: 30

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