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

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Basic information

Entry
Database: PDB / ID: 8bxu
TitleCrystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with MPD (2-Methyl-2,4-pentanediol)
ComponentsOdorant binding protein
KeywordsTRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction
Function / homologyInsect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / extracellular region / 2-ETHOXYETHANOL / Odorant binding protein
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 9, 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 16, 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

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Assembly

Deposited unit
AAA: Odorant binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5736
Polymers14,1051
Non-polymers4685
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-48 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.943, 35.509, 55.063
Angle α, β, γ (deg.)90.000, 100.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12M Monosaccharides (0.02 M each of D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D-Glucosamine), 0.1 M Bicine/Trizma base, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) ...Details: 0.12M Monosaccharides (0.02 M each of D-Glucose, D-Mannose, D-Galactose, L-Fucose, D-Xylose and N-Acetyl-D-Glucosamine), 0.1 M Bicine/Trizma base, pH 8.5, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350 and 12.5% (v/v) MPD (2-Methyl-2,4-pentanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.35→54.14 Å / Num. obs: 27461 / % possible obs: 96.5 % / Redundancy: 2.8 % / CC1/2: 0.999 / Net I/σ(I): 12.7
Reflection shellResolution: 1.35→1.42 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3964 / CC1/2: 0.749 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→33.398 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.148 / SU ML: 0.045 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1941 1393 5.075 %
Rwork0.1657 26055 -
all0.167 --
obs-27448 96.076 %
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: 21.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.772 Å20 Å20.383 Å2
2--0.138 Å20 Å2
3----0.985 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 31 126 1130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131144
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171112
X-RAY DIFFRACTIONr_angle_refined_deg1.891.6631545
X-RAY DIFFRACTIONr_angle_other_deg1.5631.5912596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.65622.07553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.11158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021291
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02229
X-RAY DIFFRACTIONr_nbd_refined0.2760.2283
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21028
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2532
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.282
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2930.29
X-RAY DIFFRACTIONr_nbd_other0.2440.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.29
X-RAY DIFFRACTIONr_mcbond_it1.8091.905564
X-RAY DIFFRACTIONr_mcbond_other1.811.906563
X-RAY DIFFRACTIONr_mcangle_it2.5942.852726
X-RAY DIFFRACTIONr_mcangle_other2.5922.852727
X-RAY DIFFRACTIONr_scbond_it3.3232.365580
X-RAY DIFFRACTIONr_scbond_other3.3212.367581
X-RAY DIFFRACTIONr_scangle_it5.0633.358819
X-RAY DIFFRACTIONr_scangle_other5.063.363820
X-RAY DIFFRACTIONr_lrange_it5.97424.2031351
X-RAY DIFFRACTIONr_lrange_other5.88523.7151329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.312940.2691898X-RAY DIFFRACTION95.6772
1.385-1.4230.3011140.2531854X-RAY DIFFRACTION95.2104
1.423-1.4640.246780.2251801X-RAY DIFFRACTION95.7208
1.509-1.5590.26880.1921749X-RAY DIFFRACTION96.1277
1.559-1.6130.199920.1781632X-RAY DIFFRACTION95.6184
1.613-1.6740.218940.1761587X-RAY DIFFRACTION96.2772
1.674-1.7430.235820.1731547X-RAY DIFFRACTION96.6192
1.743-1.820.231860.1671482X-RAY DIFFRACTION96.6112
1.82-1.9090.194740.1631418X-RAY DIFFRACTION96.6947
1.909-2.0120.191700.1611341X-RAY DIFFRACTION95.7259
2.281-2.4630.169520.1361139X-RAY DIFFRACTION96.4372
2.463-2.6980.169650.1471033X-RAY DIFFRACTION96.9965
3.015-3.480.212410.167841X-RAY DIFFRACTION95.9739
3.48-4.2570.218400.142699X-RAY DIFFRACTION95.6016
4.257-6.0020.22310.18555X-RAY DIFFRACTION96.8595

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