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- PDB-29li: Structure of Anopheles gambiae OBP9 in complex with PEG -

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Basic information

Entry
Database: PDB / ID: 29li
TitleStructure of Anopheles gambiae OBP9 in complex with PEG
ComponentsAGAP000278-PA
KeywordsTRANSPORT PROTEIN / Insect Odorant Binding Protein OBP9 Anopheles gambiae Alpha helical protein
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 19, 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

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Assembly

Deposited unit
A: AGAP000278-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3722
Polymers14,0901
Non-polymers2821
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-1 kcal/mol
Surface area6790 Å2
Unit cell
Length a, b, c (Å)35.041, 44.173, 62.087
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-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.71 Å3/Da / Density % sol: 27.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.12 M Ethylene glycols: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 30% v/v Mix 1: ...Details: 0.12 M Ethylene glycols: 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 30% v/v Mix 1: 40% v/v PEG 500* MME; 20% w/v PEG 20000

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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: 0.88559 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88559 Å / Relative weight: 1
ReflectionResolution: 1.2→62.09 Å / Num. obs: 30888 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.993 / Net I/σ(I): 17.2
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 1496 / CC1/2: 0.982 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→31.06 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.441 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2088 1501 4.9 %RANDOM
Rwork0.18389 ---
obs0.18521 29327 99.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.462 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---0.19 Å20 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.2→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 19 91 1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121015
X-RAY DIFFRACTIONr_bond_other_d0.0020.016948
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.8271372
X-RAY DIFFRACTIONr_angle_other_deg0.7251.8282191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9925126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.43455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8810178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
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_it7.7661.926484
X-RAY DIFFRACTIONr_mcbond_other7.7521.926484
X-RAY DIFFRACTIONr_mcangle_it9.7153.474607
X-RAY DIFFRACTIONr_mcangle_other9.7123.478608
X-RAY DIFFRACTIONr_scbond_it7.2822.335531
X-RAY DIFFRACTIONr_scbond_other7.2762.336532
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.444.115762
X-RAY DIFFRACTIONr_long_range_B_refined16.15725.951208
X-RAY DIFFRACTIONr_long_range_B_other16.10124.991194
X-RAY DIFFRACTIONr_rigid_bond_restr4.16331963
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
Rfree0.256 100 -
Rwork0.211 2132 -
obs--99.96 %

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