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- PDB-6p2e: Structure of Aedes aegypti OBP22 in the complex with benzaldehyde -

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Basic information

Entry
Database: PDB / ID: 6p2e
TitleStructure of Aedes aegypti OBP22 in the complex with benzaldehyde
ComponentsOBP22, AAEL005772-PA
KeywordsTRANSPORT PROTEIN / Odorant binding protein / Chemo-sensory signaling
Function / homologyInsect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / lipid binding / BENZOIC ACID / Odorant binding protein
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 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 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: OBP22, AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8996
Polymers14,4001
Non-polymers4985
Water1,982110
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)86.934, 86.934, 58.515
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-205-

SO4

21A-308-

HOH

31A-341-

HOH

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Components

#1: Protein OBP22, 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-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 4.61 Å3/Da / Density % sol: 73.4 %
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 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 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 40781 / % possible obs: 99.69 % / Redundancy: 2 % / Biso Wilson estimate: 30.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01588 / Rpim(I) all: 0.01588 / Rrim(I) all: 0.02246 / Net I/σ(I): 25.63
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2494 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 2001 / CC1/2: 0.889 / Rpim(I) all: 0.2494 / Rrim(I) all: 0.3528 / % possible all: 99.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OBP22 structure solved by tantalum SAD

Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.269 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20013 1997 9.8 %RANDOM
Rwork0.18294 ---
obs0.18464 18421 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.491 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 31 110 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181015
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.6381472
X-RAY DIFFRACTIONr_angle_other_deg0.3951.5912314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.98723.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66115190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.353156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
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_it2.263.21509
X-RAY DIFFRACTIONr_mcbond_other2.2633.2508
X-RAY DIFFRACTIONr_mcangle_it3.394.785642
X-RAY DIFFRACTIONr_mcangle_other3.3874.798643
X-RAY DIFFRACTIONr_scbond_it3.153.632577
X-RAY DIFFRACTIONr_scbond_other3.1233.584570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9735.22818
X-RAY DIFFRACTIONr_long_range_B_refined6.58538.4751292
X-RAY DIFFRACTIONr_long_range_B_other6.58238.4841293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 141 -
Rwork0.255 1322 -
obs--97.99 %

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