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- PDB-6otl: Structure of Aedes aegypti OBP22 in the complex with benzaldehyde -

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Basic information

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


odorant binding / sensory perception of smell / lipid binding / :
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
BENZOIC ACID / PHOSPHATE ION / HEXATANTALUM DODECABROMIDE / Odorant-binding protein 22
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsJones, D.N. / Murphy, E.
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
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: 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 1.3Oct 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 / _database_2.pdbx_database_accession

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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)16,6624
Polymers14,4001
Non-polymers2,2623
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, NMR relaxation experiments establish the overall correlation time is consistent with the presence of a monomeric species in solution. The dimeric form appears to ...Evidence: assay for oligomerization, NMR relaxation experiments establish the overall correlation time is consistent with the presence of a monomeric species in solution. The dimeric form appears to be a crystallization artifact.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.760, 87.760, 59.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: pET13a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1HRL7
#2: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2M Ammonium sulfate, 0.1 M sodium citrate, 0.2M sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.254 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 13, 2013 / Details: Rosenbaum-Rock monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.254 Å / Relative weight: 1
ReflectionResolution: 2.59→25 Å / Num. obs: 8456 / % possible obs: 99.44 % / Redundancy: 2 % / Biso Wilson estimate: 56.58 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.06703 / Rpim(I) all: 0.06703 / Rrim(I) all: 0.09479 / Net I/σ(I): 27.32
Reflection shellResolution: 2.591→2.684 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2885 / Mean I/σ(I) obs: 3.23 / Num. unique obs: 798 / CC1/2: 0.828 / Rpim(I) all: 0.2885 / Rrim(I) all: 0.408 / % possible all: 96.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.805 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.20913 841 9.9 %RANDOM
Rwork0.19354 ---
obs0.19512 7614 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.29 Å20 Å2
2--0.57 Å20 Å2
3----1.86 Å2
Refinement stepCycle: 1 / Resolution: 2.59→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 32 6 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.7971543
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.22823.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60215170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.481155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02771
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1565.122483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.8557.663602
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7915.501559
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.03866.4941428
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.591→2.658 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 58 -
Rwork0.369 524 -
obs--95.72 %

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