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- PDB-8c68: CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAM... -

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Basic information

Entry
Database: PDB / ID: 8c68
TitleCRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAMBIAE (AGAMOBP4) AT PH 4.6
ComponentsAGAP010489-PA
KeywordsTRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction
Function / homology
Function and homology information


dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / extracellular region / metal ion binding
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
ACETATE ION / AGAP010489-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTsitsanou, K.E. / Drakou, C.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: Influence of pH on indole-dependent heterodimeric interactions between Anopheles gambiae odorant-binding proteins OBP1 and OBP4.
Authors: Mam, B. / Tsitsanou, K.E. / Liggri, P.G.V. / Saitta, F. / Stamati, E.C.V. / Mahita, J. / Leonis, G. / Drakou, C.E. / Papadopoulos, M. / Arnaud, P. / Offmann, B. / Fessas, D. / Sowdhamini, R. / Zographos, S.E.
History
DepositionJan 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Feb 14, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: 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
A: AGAP010489-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5147
Polymers14,0491
Non-polymers4656
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-27 kcal/mol
Surface area6990 Å2
Unit cell
Length a, b, c (Å)51.800, 51.800, 87.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AGAP010489-PA / Odorant binding protein / Odorant-binding protein AgamOBP4 / Odorant-binding protein antennal 4


Mass: 14048.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: OBP-4, 1275228, AgamOBP4, OBP4, AgaP_AGAP010489, agCG48601
Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB(DE3) / References: UniProt: Q8T6R7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 48.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 2.0 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2009 / Details: MULTILAYER MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2.05→44.86 Å / Num. obs: 8929 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Net I/σ(I): 21.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6 / Num. unique obs: 1270 / CC1/2: 0.942 / Rpim(I) all: 0.13 / Rrim(I) all: 0.384 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N88

3n88
PDB Unreleased entry


Resolution: 2.05→44.86 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.67 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 421 4.7 %RANDOM
Rwork0.185 ---
obs0.187 8889 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.05→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 27 66 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2232.0011419
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4595137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56725.64139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48215202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.489152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021791
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5491.5664
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03821077
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8263381
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8964.5342
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 37 -
Rwork0.181 581 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
129.9404-2.32992.68918.5752-4.469416.3816-0.09160.8653-0.8623-0.86920.42822.2187-0.2935-0.7045-0.33660.0732-0.0137-0.25050.03920.07040.686111.5121-7.713822.1641
20.86740.4653-0.24412.71160.73912.5212-0.03590.01430.0575-0.06680.08090.0449-0.14610.037-0.0450.08080.0034-0.02490.0931-0.00830.11924.7557-5.517521.6773
33.0253-0.03230.8952.29330.21133.17360.03340.01860.04560.0084-0.00710.01020.13450.0127-0.02630.1134-0.04030.02380.116-0.01270.119717.6631-19.922713.4541
45.1303-0.3423.43010.13170.81015.71620.08320.1294-0.07610.03470.0482-0.03230.32520.1277-0.13140.1435-0.02160.00790.1337-0.01940.092927.2843-19.67888.3181
52.3135-0.2770.46952.9054-0.29133.8459-0.05240.14040.0332-0.03120.11420.0061-0.07790.302-0.06180.0882-0.01020.00260.1276-0.01420.111929.2984-13.388214.8598
64.8615-2.5596-8.9722-4.66414.224617.87990.23210.49030.3097-0.1296-0.61340.0602-1.6625-0.90470.38140.4682-0.0184-0.3580.12660.03260.398218.1992-8.705710.5312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 16
2X-RAY DIFFRACTION2A17 - 54
3X-RAY DIFFRACTION3A55 - 83
4X-RAY DIFFRACTION4A84 - 100
5X-RAY DIFFRACTION5A101 - 118
6X-RAY DIFFRACTION6A119 - 125

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