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- PDB-29ly: Structure of Anopheles gambiae OBP9 in complex with n-Butyl cinnamate -

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Basic information

Entry
Database: PDB / ID: 29ly
TitleStructure of Anopheles gambiae OBP9 in complex with n-Butyl cinnamate
ComponentsAGAP000278-PA
KeywordsTRANSPORT PROTEIN / Insect Odorant Binding Protein OBP9 Anopheles gambiae n-Butyl cinnamate
Function / homologyInsect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / sensory perception of smell / : / : / Uncharacterized protein
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsChristodoulou, E. / Stamati, E.C.V. / Tsitsanou, K.E. / Zographos, S.E.
Funding support Greece, European Union, 3items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)HFRI FM17 637 Greece
General Secretariat for Research and Technology (GSRT)MIS 5002550European Union
iNEXT-DiscoveryGA 871037European Union
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural insights into ligand recognition by the pleiotropic odorant-binding protein AgamOBP9.
Authors: Christodoulou, E. / Stamati, E.C.V. / Saitta, F. / Papakyriakou, A. / Fessas, D. / Tsitsanou, K.E. / Zographos, S.E.
History
DepositionMar 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGAP000278-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4615
Polymers14,0901
Non-polymers3714
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-5 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.223, 45.182, 64.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AGAP000278-PA / Odorant-binding protein AgamOBP9


Mass: 14089.935 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: AgamOBP9, 1271980, OBP9, AgaP_AGAP000278 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I8R2
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-A1J28 / Butyl Cinnamate / butyl (E)-3-phenylprop-2-enoate


Mass: 204.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.66 Å3/Da / Density % sol: 25.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06 M Divalents : 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 37.5% v/v Mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.2→45.18 Å / Num. obs: 30092 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.032 / Rrim(I) all: 0.113 / Net I/σ(I): 15.4 / Num. measured all: 376660
Reflection shellResolution: 1.2→1.26 Å / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.235 / Num. measured all: 52997 / Num. unique obs: 4333 / CC1/2: 0.98 / Rpim(I) all: 0.069 / Rrim(I) all: 0.245 / Net I/σ(I) obs: 8.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→36.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.942 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15597 1507 5 %RANDOM
Rwork0.13662 ---
obs0.1376 28521 99.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2--0.14 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.2→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 25 99 1085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121087
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161006
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.8391485
X-RAY DIFFRACTIONr_angle_other_deg0.6011.8212325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6015140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.79757
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50410191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.3620.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021341
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02267
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_it4.0161.17513
X-RAY DIFFRACTIONr_mcbond_other3.9771.169513
X-RAY DIFFRACTIONr_mcangle_it5.8172.101650
X-RAY DIFFRACTIONr_mcangle_other5.8232.104651
X-RAY DIFFRACTIONr_scbond_it5.7521.442574
X-RAY DIFFRACTIONr_scbond_other5.7481.442575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2792.533829
X-RAY DIFFRACTIONr_long_range_B_refined12.4317.421359
X-RAY DIFFRACTIONr_long_range_B_other11.83816.231336
X-RAY DIFFRACTIONr_rigid_bond_restr3.88632093
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 121 -
Rwork0.122 2075 -
obs--99.95 %

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