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- PDB-29md: Structure of Anopheles gambiae OBP9 in complex with PMD (P-Mentha... -

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Basic information

Entry
Database: PDB / ID: 29md
TitleStructure of Anopheles gambiae OBP9 in complex with PMD (P-Menthane-3,8-diol)
ComponentsAGAP000278-PA
KeywordsTRANSPORT PROTEIN / Insect Odorant Binding Protein OBP9 Anopheles gambiae PMD (P-Menthane-3 / 8-diol)
Function / homology
Function and homology information


odorant binding / sensory perception of smell / :
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
: / TRIETHYLENE GLYCOL / Uncharacterized protein
Similarity search - Component
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)14,4123
Polymers14,0901
Non-polymers3222
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint6 kcal/mol
Surface area6830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.341, 43.959, 62.055
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) / Strain (production host): Origami 2 (DE3) / References: UniProt: Q8I8R2
#2: Chemical ChemComp-A1J26 / P-Menthane-3,8-diol / (1R,2S,5S)-5-methyl-2-(2-oxidanylpropan-2-yl)cyclohexan-1-ol / (1R,2S,5S)-2-(2-hydroxypropan-2-yl)-5-methylcyclohexan-1-ol


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 28.09 %
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→62.05 Å / Num. obs: 30763 / % possible obs: 99.2 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Χ2: 0.99 / Net I/σ(I): 17.5 / Num. measured all: 398443
Reflection shellResolution: 1.2→1.22 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.402 / Num. measured all: 20262 / Num. unique obs: 1513 / CC1/2: 0.985 / Rpim(I) all: 0.112 / Rrim(I) all: 0.418 / Χ2: 1.03 / Net I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.551 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19859 1492 4.9 %RANDOM
Rwork0.16725 ---
obs0.1689 29198 99.18 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.785 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0 Å2-0 Å2
2--0.16 Å20 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 1.2→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 22 94 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121072
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161007
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.8341462
X-RAY DIFFRACTIONr_angle_other_deg0.9611.8162335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9995137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.68755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39210193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1980.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
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_it5.0821.848508
X-RAY DIFFRACTIONr_mcbond_other5.0521.847508
X-RAY DIFFRACTIONr_mcangle_it7.153.324642
X-RAY DIFFRACTIONr_mcangle_other7.1573.328643
X-RAY DIFFRACTIONr_scbond_it6.4772.247564
X-RAY DIFFRACTIONr_scbond_other6.4732.25565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2123.969814
X-RAY DIFFRACTIONr_long_range_B_refined12.61222.991292
X-RAY DIFFRACTIONr_long_range_B_other12.42321.841274
X-RAY DIFFRACTIONr_rigid_bond_restr3.47732079
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
Rfree0.228 106 -
Rwork0.2 2143 -
obs--99.78 %

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