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- PDB-6omw: Structure of Aedes aegypti OBP22 in the complex with palmitoleic acid -

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Basic information

Entry
Database: PDB / ID: 6omw
TitleStructure of Aedes aegypti OBP22 in the complex with palmitoleic 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
MALONIC ACID / PALMITOLEIC ACID / Odorant-binding protein 22
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 19, 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 30, 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
A: AAEL005772-PA
B: AAEL005772-PA
F: AAEL005772-PA
C: AAEL005772-PA
D: AAEL005772-PA
I: AAEL005772-PA
G: AAEL005772-PA
H: AAEL005772-PA
E: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,09519
Polymers129,6039
Non-polymers1,49210
Water6,053336
1
A: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5042
Polymers14,4001
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5042
Polymers14,4001
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6552
Polymers14,4001
Non-polymers2541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5042
Polymers14,4001
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5042
Polymers14,4001
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
I: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6552
Polymers14,4001
Non-polymers2541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5042
Polymers14,4001
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6083
Polymers14,4001
Non-polymers2082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
E: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6552
Polymers14,4001
Non-polymers2541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.214, 154.214, 58.163
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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-PAM / PALMITOLEIC ACID


Mass: 254.408 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H30O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.08 Å3/Da / Density % sol: 60.12 % / Description: hexagon stick
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 1.4M ammonium sulfate, 0.1M citric acid

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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: Sep 18, 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, L10.736
11-K, -H, -L20.264
ReflectionResolution: 2.1→38.55 Å / Num. obs: 89691 / % possible obs: 97.45 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.23 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.07469 / Rpim(I) all: 0.03782 / Rrim(I) all: 0.08434 / Net I/σ(I): 12.39
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4459 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 7315 / CC1/2: 0.712 / Rpim(I) all: 0.3608 / Rrim(I) all: 0.5761 / % possible all: 80.92

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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: 2.1→38.55 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.518 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.038 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24688 4398 5.1 %RANDOM
Rwork0.21053 ---
obs0.21235 81980 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.226 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.15 Å2
Refinement stepCycle: 1 / Resolution: 2.1→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8733 0 103 336 9172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0129054
X-RAY DIFFRACTIONr_bond_other_d0.0010.0188406
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.64812230
X-RAY DIFFRACTIONr_angle_other_deg0.3541.58419225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83251074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.35123.654509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.806151580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6681543
X-RAY DIFFRACTIONr_chiral_restr0.0510.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022138
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_it1.7262.874320
X-RAY DIFFRACTIONr_mcbond_other1.7252.874319
X-RAY DIFFRACTIONr_mcangle_it2.7424.2885386
X-RAY DIFFRACTIONr_mcangle_other2.7414.2885387
X-RAY DIFFRACTIONr_scbond_it2.0333.1064734
X-RAY DIFFRACTIONr_scbond_other2.0333.1054732
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3174.5536844
X-RAY DIFFRACTIONr_long_range_B_refined4.86733.86210571
X-RAY DIFFRACTIONr_long_range_B_other4.79433.7210511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 228 -
Rwork0.42 4307 -
obs--67.49 %

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