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- PDB-8bxv: Crystal structure of Odorant Binding Protein 5 from Anopheles gam... -

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Basic information

Entry
Database: PDB / ID: 8bxv
TitleCrystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Thymol
ComponentsOdorant binding protein
KeywordsTRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction / Thymol
Function / homology
Function and homology information


odorant binding / extracellular region
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
5-METHYL-2-(1-METHYLETHYL)PHENOL / DI(HYDROXYETHYL)ETHER / R-1,2-PROPANEDIOL / Odorant binding protein
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLiggri, P.G.V. / Tsitsanou, K.E. / Zographos, S.E.
Funding support Greece, 2items
OrganizationGrant numberCountry
Other governmentT1EDK-00996 Greece
Other governmentMIS5000432 Greece
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: The structure of AgamOBP5 in complex with the natural insect repellents Carvacrol and Thymol: Crystallographic, fluorescence and thermodynamic binding studies.
Authors: Liggri, P.G.V. / Tsitsanou, K.E. / Stamati, E.C.V. / Saitta, F. / Drakou, C.E. / Leonidas, D.D. / Fessas, D. / Zographos, S.E.
History
DepositionDec 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 12, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Odorant binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6027
Polymers14,1051
Non-polymers4976
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-17 kcal/mol
Surface area6730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.241, 36.566, 54.962
Angle α, β, γ (deg.)90.000, 100.383, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Odorant binding protein


Mass: 14105.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: OBP-5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8T6R6

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Non-polymers , 6 types, 132 molecules

#2: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-IPB / 5-METHYL-2-(1-METHYLETHYL)PHENOL


Mass: 150.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% ...Details: 0.12M alcohols (0.02 M each of 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol (racemic), 2-Propanol, 1,4- Butanediol and 1,3-Propanediol), 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.3→54.06 Å / Num. obs: 31153 / % possible obs: 94.3 % / Redundancy: 6.4 % / CC1/2: 0.999 / Net I/σ(I): 22.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.7 % / Num. unique obs: 4715 / CC1/2: 0.98 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→54.06 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.837 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2202 1581 5.077 %
Rwork0.1851 29559 -
all0.187 --
obs-31140 93.948 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.221 Å20 Å20.265 Å2
2--0.89 Å20 Å2
3----0.719 Å2
Refinement stepCycle: LAST / Resolution: 1.3→54.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 33 126 1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131182
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171141
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.6691594
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5992644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47621.2962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10515242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4191511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02252
X-RAY DIFFRACTIONr_nbd_refined0.2950.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21079
X-RAY DIFFRACTIONr_nbtor_refined0.180.2544
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.297
X-RAY DIFFRACTIONr_metal_ion_refined0.120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.23
X-RAY DIFFRACTIONr_nbd_other0.20.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.214
X-RAY DIFFRACTIONr_mcbond_it1.8032.08569
X-RAY DIFFRACTIONr_mcbond_other1.8072.082570
X-RAY DIFFRACTIONr_mcangle_it2.6013.128734
X-RAY DIFFRACTIONr_mcangle_other2.63.127735
X-RAY DIFFRACTIONr_scbond_it2.9962.52613
X-RAY DIFFRACTIONr_scbond_other2.9942.521614
X-RAY DIFFRACTIONr_scangle_it4.3493.631860
X-RAY DIFFRACTIONr_scangle_other4.3473.632861
X-RAY DIFFRACTIONr_lrange_it6.09726.8541467
X-RAY DIFFRACTIONr_lrange_other6.00626.4061440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.334-1.370.2541150.2342239X-RAY DIFFRACTION97.6358
1.37-1.410.2431050.2292148X-RAY DIFFRACTION97.6593
1.41-1.4530.2431080.2122059X-RAY DIFFRACTION98.0987
1.453-1.5010.2281120.1942035X-RAY DIFFRACTION98.2609
1.501-1.5540.2141150.1881960X-RAY DIFFRACTION98.2481
1.554-1.6120.211230.1851859X-RAY DIFFRACTION97.8765
1.612-1.6780.219890.1831833X-RAY DIFFRACTION98.4127
1.678-1.7530.22940.1891753X-RAY DIFFRACTION98.8229
1.753-1.8380.2211060.1831680X-RAY DIFFRACTION98.4565
1.838-1.9370.221520.1951215X-RAY DIFFRACTION74.1369
1.937-2.0550.188670.1881341X-RAY DIFFRACTION87.0748
2.055-2.1960.214550.1681153X-RAY DIFFRACTION79.3693
2.196-2.3720.164570.1621095X-RAY DIFFRACTION81.2985
2.372-2.5980.241640.1651238X-RAY DIFFRACTION98.6364
2.598-2.9040.221520.18986X-RAY DIFFRACTION87.8173
2.904-3.3510.218440.1891003X-RAY DIFFRACTION99.3359
3.351-4.10.216400.169713X-RAY DIFFRACTION84.0402
4.1-5.7820.207360.179660X-RAY DIFFRACTION98.0282

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