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- PDB-9j00: Crystal Structure Sensory Appendage Protein 2 from Anopheles culi... -

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Basic information

Entry
Database: PDB / ID: 9j00
TitleCrystal Structure Sensory Appendage Protein 2 from Anopheles culicifacies in space group P21 with three molecules per ASU
ComponentsChemosensory protein 3
KeywordsLIPID BINDING PROTEIN / Sensory Appendage Protein 2 / SAP2 / Mosquito / Olfaction / hydrophobic chemicals / Vector Control
Function / homologyInsect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 superfamily / Insect pheromone-binding family, A10/OS-D / ACETATE ION / : / Chemosensory protein 3
Function and homology information
Biological speciesAnopheles culicifacies (mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.828 Å
AuthorsGoswami, R. / Biswas, S. / Chakraborti, S. / Manickam, Y.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)PR32713 India
Indian Council of Medical Research75/20/2020/ECD-II India
CitationJournal: To Be Published
Title: Crystal Structure and Ligand Binding Studies of Chemosensory and Sensory Appendage Proteins
Authors: Biswas, S. / Goswami, R. / Barbosa, R.L. / Sung, S. / Marquez, J.A. / Chakraborti, S. / Manickam, Y.
History
DepositionAug 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chemosensory protein 3
B: Chemosensory protein 3
C: Chemosensory protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,56427
Polymers39,4593
Non-polymers2,10624
Water4,360242
1
A: Chemosensory protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,99311
Polymers13,1531
Non-polymers84010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5230 Å2
MethodPISA
2
B: Chemosensory protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8989
Polymers13,1531
Non-polymers7458
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area6050 Å2
MethodPISA
3
C: Chemosensory protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6737
Polymers13,1531
Non-polymers5216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.504, 37.345, 79.437
Angle α, β, γ (deg.)90.00, 96.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chemosensory protein 3


Mass: 13152.870 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles culicifacies (mosquito) / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A182MAD2
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Lithium chloride, 0.1 M Sodium acetate pH 4.5, 30% v/v PEG 400, 0.1 M Cadmium chloride hemi(pentahydrate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.828→78.968 Å / Num. obs: 30282 / % possible obs: 98.9 % / Redundancy: 5.4 % / CC1/2: 0.996 / Rrim(I) all: 0.15 / Net I/σ(I): 8.5
Reflection shellResolution: 1.828→1.86 Å / Redundancy: 3.7 % / Num. unique obs: 1306 / CC1/2: 0.358 / Rrim(I) all: 1.932 / % possible all: 86.8

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Processing

Software
NameVersionClassification
PHENIX(1.15rc1_3423: ???)refinement
autoPROCdata scaling
CRANK2phasing
autoPROCdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.828→78.968 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 1508 4.99 %
Rwork0.1903 --
obs0.1925 30195 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.828→78.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 27 242 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112501
X-RAY DIFFRACTIONf_angle_d1.3033369
X-RAY DIFFRACTIONf_dihedral_angle_d6.3751963
X-RAY DIFFRACTIONf_chiral_restr0.064360
X-RAY DIFFRACTIONf_plane_restr0.007445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8282-1.88720.31751250.292246X-RAY DIFFRACTION86
1.8872-1.95470.25381210.23932569X-RAY DIFFRACTION98
1.9547-2.0330.24631310.21172637X-RAY DIFFRACTION100
2.033-2.12550.23321520.19222572X-RAY DIFFRACTION100
2.1255-2.23750.24091340.18282659X-RAY DIFFRACTION100
2.2375-2.37770.23391340.18252622X-RAY DIFFRACTION100
2.3777-2.56130.22711480.16972648X-RAY DIFFRACTION100
2.5613-2.81910.20981390.16972629X-RAY DIFFRACTION100
2.8191-3.22710.22361410.1772663X-RAY DIFFRACTION100
3.2271-4.06570.22611400.16812684X-RAY DIFFRACTION100
4.0657-78.9680.25021430.21032758X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.97 Å / Origin y: -16.0311 Å / Origin z: 12.5174 Å
111213212223313233
T0.1248 Å2-0.0218 Å20.0198 Å2-0.1322 Å20.0086 Å2--0.1104 Å2
L0.2651 °2-0.1912 °20.1318 °2-0.1965 °2-0.0429 °2--0.0955 °2
S0.0022 Å °-0.0201 Å °-0.0198 Å °0.0348 Å °0.0073 Å °0.0446 Å °-0.0263 Å °0.0095 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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