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- PDB-8c6e: CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAM... -

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Basic information

Entry
Database: PDB / ID: 8c6e
TitleCRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 4 FROM ANOPHELES GAMBIAE (AGAMOBP4) AT PH 8.5
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGAP010489-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1293
Polymers14,0491
Non-polymers802
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area7100 Å2
Unit cell
Length a, b, c (Å)33.950, 55.580, 56.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% W/V PEG 8000, 0.2 M MAGNESIUM CHLORIDE, 0.1 M TRIS-HCL PH 8.5,

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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→39.54 Å / Num. obs: 7086 / % possible obs: 99.8 % / Redundancy: 7 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Net I/σ(I): 21.2
Reflection shellResolution: 2.05→2.16 Å / % possible obs: 100 % / Redundancy: 7.1 % / Num. measured all: 7131 / Num. unique obs: 1001 / Rpim(I) all: 0.067 / Rrim(I) all: 0.183 / Net I/σ(I) obs: 9.8

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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→39.54 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.383 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 333 4.7 %RANDOM
Rwork0.19 ---
obs0.192 7045 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 2 70 1035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9871375
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1825132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66125.78938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8515207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.148152
X-RAY DIFFRACTIONr_chiral_restr0.0940.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021747
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_it0.4251.5646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74621045
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.683375
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4834.5327
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
Rfree0.303 23 -
Rwork0.179 480 -
obs--99.8 %
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)
110.936-1.3979-1.47751.78110.11442.94310.1876-0.19630.0257-0.081-0.0538-0.02070.0595-0.0804-0.13380.1217-0.00520.0030.0526-0.01150.0571-3.52968.292-29.3135
22.32660.764-0.12044.56370.15144.57310.09240.0810.20490.141-0.01740.2335-0.3427-0.0989-0.0750.05230.01510.01470.049100.0396-9.175815.1146-21.717
310.79462.909-5.32242.24462.057811.1361-0.29940.1228-0.29250.0009-0.30090.21960.3682-0.63790.60030.28310.05390.00170.1807-0.05990.3877-10.1496-1.2786-15.7897
410.42070.856-4.26885.05110.89198.4188-0.0578-0.0613-0.16620.03490.1119-0.1970.03560.097-0.05420.11780.0044-0.0350.01380.00010.06341.6651-1.1024-14.1359
58.4627-0.5928-2.41531.96950.79443.78530.0214-0.076-0.23430.1924-0.0347-0.0877-0.0144-0.05120.01330.07-0.0097-0.03160.01050.01650.06281.58447.7336-10.5504
63.64131.2647-0.64123.9254-1.19792.02730.155-0.22690.15870.2459-0.15370.2377-0.1287-0.0397-0.00130.06130.00780.01760.0388-0.01730.0204-8.291511.8378-12.0748
72.72824.03132.59586.0153.82212.4733-0.20620.5534-0.2993-0.16440.5715-0.4583-0.13690.5666-0.36520.2292-0.10170.08330.6115-0.05650.30492.796713.5854-18.9628
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 25
2X-RAY DIFFRACTION2A26 - 53
3X-RAY DIFFRACTION3A54 - 64
4X-RAY DIFFRACTION4A65 - 77
5X-RAY DIFFRACTION5A78 - 100
6X-RAY DIFFRACTION6A101 - 117
7X-RAY DIFFRACTION7A118 - 125

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