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- PDB-6opb: Structure of Aedes aegypti OBP22 in the complex with arachidic acid -

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Basic information

Entry
Database: PDB / ID: 6opb
TitleStructure of Aedes aegypti OBP22 in the complex with arachidic 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 / :
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
icosanoic acid / Odorant-binding protein 22
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
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
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: AAEL005772-PA
A: AAEL005772-PA
B: AAEL005772-PA
F: AAEL005772-PA
C: AAEL005772-PA
D: AAEL005772-PA
G: AAEL005772-PA
H: AAEL005772-PA
I: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,61913
Polymers129,6039
Non-polymers1,0164
Water2,972165
1
E: AAEL005772-PA
hetero molecules


  • defined by author
  • 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.
  • 14.7 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)14,7132
Polymers14,4001
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AAEL005772-PA


Theoretical massNumber of molelcules
Total (without water)14,4001
Polymers14,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4782
Polymers14,4001
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7132
Polymers14,4001
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: AAEL005772-PA


Theoretical massNumber of molelcules
Total (without water)14,4001
Polymers14,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: AAEL005772-PA


Theoretical massNumber of molelcules
Total (without water)14,4001
Polymers14,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: AAEL005772-PA


Theoretical massNumber of molelcules
Total (without water)14,4001
Polymers14,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: AAEL005772-PA


Theoretical massNumber of molelcules
Total (without water)14,4001
Polymers14,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7132
Polymers14,4001
Non-polymers3131
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.259, 154.259, 58.043
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
AAEL005772-PA / Odorant binding protein


Mass: 14400.319 Da / Num. of mol.: 9
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-DCR / icosanoic acid


Mass: 312.530 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C20H40O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.14 Å3/Da / Density % sol: 60.86 % / Description: hexagon stick
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 1.55M ammonium sulfate, 0.1M citric acid, 0.5M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS3 X 200K-A / Detector: PIXEL / Date: Aug 2, 2018 / Details: VariMax Cu-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.505
11-K, -H, -L20.495
ReflectionResolution: 2→38.56 Å / Num. obs: 102184 / % possible obs: 99.91 % / Redundancy: 3.2 % / Biso Wilson estimate: 23.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04284 / Rpim(I) all: 0.02153 / Rrim(I) all: 0.04836 / Net I/σ(I): 30.17
Reflection shellResolution: 2→2.072 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.1576 / Mean I/σ(I) obs: 6.42 / Num. unique obs: 10406 / CC1/2: 0.916 / Rpim(I) all: 0.1356 / Rrim(I) all: 0.2089 / % possible all: 99.62

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OBP22 structure slved by tantalum SAD

Resolution: 2→38.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.006 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 5022 4.9 %RANDOM
Rwork0.17647 ---
obs0.17847 97388 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.715 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 2→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8749 0 70 165 8984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0188434
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.64812242
X-RAY DIFFRACTIONr_angle_other_deg0.3571.60219289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90551086
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.86923.597506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.411151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9161545
X-RAY DIFFRACTIONr_chiral_restr0.050.21182
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022155
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_it1.4122.8174359
X-RAY DIFFRACTIONr_mcbond_other1.4112.8174358
X-RAY DIFFRACTIONr_mcangle_it2.2154.2125437
X-RAY DIFFRACTIONr_mcangle_other2.2144.2125438
X-RAY DIFFRACTIONr_scbond_it1.4272.9264694
X-RAY DIFFRACTIONr_scbond_other1.4262.9264695
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2724.336805
X-RAY DIFFRACTIONr_long_range_B_refined3.5632.73210490
X-RAY DIFFRACTIONr_long_range_B_other3.55232.72810470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 359 -
Rwork0.223 6882 -
obs--93.89 %

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