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

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Basic information

Entry
Database: PDB / ID: 6oii
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 / 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
ARACHIDONIC ACID / : / : / Odorant binding protein
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.85 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 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AAEL005772-PA
B: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,04512
Polymers28,8012
Non-polymers1,24410
Water3,189177
1
A: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9976
Polymers14,4001
Non-polymers5975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0476
Polymers14,4001
Non-polymers6475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.210, 40.844, 56.278
Angle α, β, γ (deg.)90.00, 117.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

EDO

21A-331-

HOH

31A-396-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AAEL005772-PA / Odorant binding protein


Mass: 14400.319 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 187 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACD / ARACHIDONIC ACID / Arachidonic acid


Mass: 304.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32O2
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Co
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.97 Å3/Da / Density % sol: 37.65 % / Description: plate
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350 12 w/v, 0.1M sodium HEPES, 10mM cadmium chloride, 6mM cobalt chloride, 6mM magnesium 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: Nov 7, 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
ReflectionResolution: 1.85→27.9 Å / Num. obs: 19395 / % possible obs: 99.41 % / Redundancy: 14.6 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.02954 / Rrim(I) all: 0.114 / Net I/σ(I): 17.88
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.7619 / Mean I/σ(I) obs: 4.15 / Num. unique obs: 1900 / CC1/2: 0.929 / Rpim(I) all: 0.2127 / Rrim(I) all: 0.7922 / % possible all: 99.01

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→27.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.762 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.156 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22579 1927 10 %RANDOM
Rwork0.18918 ---
obs0.19283 17296 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0.07 Å2
2--0.6 Å20 Å2
3----0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.85→27.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 55 177 2184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122085
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181936
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.6632814
X-RAY DIFFRACTIONr_angle_other_deg0.4971.634413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5215248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78923.846117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9441510
X-RAY DIFFRACTIONr_chiral_restr0.0610.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02504
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_it0.7351.852989
X-RAY DIFFRACTIONr_mcbond_other0.7341.85988
X-RAY DIFFRACTIONr_mcangle_it1.1862.7691238
X-RAY DIFFRACTIONr_mcangle_other1.1862.7721239
X-RAY DIFFRACTIONr_scbond_it0.9952.0421096
X-RAY DIFFRACTIONr_scbond_other0.9952.0431097
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6393.0021577
X-RAY DIFFRACTIONr_long_range_B_refined3.96328.8242467
X-RAY DIFFRACTIONr_long_range_B_other3.90228.5682436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 145 -
Rwork0.276 1183 -
obs--94.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.00571.5146-0.4894.5007-1.83241.98990.2137-0.2507-0.06530.2548-0.2388-0.1986-0.17350.16120.02510.0775-0.0458-0.01780.04050.01040.04136.880224.300631.8417
29.12292.9266-4.30022.9148-0.57215.2978-0.1417-0.44110.5890.0237-0.09340.2944-0.4754-0.17190.23520.20340.0926-0.02850.0771-0.08450.17127.195135.486127.3094
32.35720.67420.18982.3929-0.89042.5226-0.01760.2035-0.22430.072-0.0568-0.0937-0.0888-0.09760.07440.0222-0.00630.02310.0376-0.03090.058331.375320.784922.4425
43.47341.45741.45632.6679-0.36064.4570.0747-0.6016-0.37930.1108-0.0192-0.22870.3683-0.3809-0.05550.08-0.0260.00950.14450.06230.131625.77318.213334.3288
51.72490.69030.01591.8921-0.7882.298-0.10450.2643-0.2204-0.15220.13610.040.1444-0.2233-0.03150.0443-0.02760.02030.0696-0.04570.06924.731615.623918.4121
63.0831-0.11213.27842.3648-1.03089.6072-0.0063-0.1548-0.01260.1850.02760.0928-0.2348-0.3875-0.02130.03090.00340.02930.0430.00240.050821.28818.605931.5573
72.1915-3.4804-0.08016.65771.32131.28680.3080.1902-0.1307-0.6609-0.29560.2364-0.16060.0318-0.01240.12670.0504-0.05940.0497-0.04760.08157.33325.1657-7.6489
86.8285-0.7879-2.22721.6082-0.54933.86680.0477-0.0520.2908-0.2065-0.1188-0.0457-0.32280.14960.07110.1037-0.00130.0020.0172-0.01330.074513.273836.24681.6963
90.8821-0.34260.03112.65521.20231.7804-0.0183-0.10590.0037-0.1483-0.00840.0977-0.0479-0.0680.02670.01250.0097-0.01190.0321-0.01690.018912.455320.59791.5359
101.0742-0.438-0.21011.83422.27775.39170.0553-0.1117-0.10960.04020.0802-0.09720.21680.0522-0.13550.02460.0101-0.01440.0475-0.0070.034320.884410.55170.3708
113.8101-1.1661-0.62312.59371.46532.1964-0.0596-0.38920.1501-0.01440.1675-0.047-0.01540.1241-0.10790.00570.0117-0.00370.075-0.02680.013617.908321.37677.8427
129.4663-1.83857.64421.98081.365511.2152-0.06250.29750.2598-0.37820.1342-0.2172-0.67390.5578-0.07180.1909-0.07730.05560.0425-0.01630.027421.369121.4842-8.4422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 22
2X-RAY DIFFRACTION2A23 - 36
3X-RAY DIFFRACTION3A37 - 69
4X-RAY DIFFRACTION4A70 - 80
5X-RAY DIFFRACTION5A81 - 106
6X-RAY DIFFRACTION6A107 - 121
7X-RAY DIFFRACTION7B2 - 18
8X-RAY DIFFRACTION8B19 - 36
9X-RAY DIFFRACTION9B37 - 74
10X-RAY DIFFRACTION10B75 - 94
11X-RAY DIFFRACTION11B95 - 108
12X-RAY DIFFRACTION12B109 - 123

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