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- PDB-8by4: Crystal structure of Odorant Binding Protein 1 from Aedes albopic... -

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Basic information

Entry
Database: PDB / ID: 8by4
TitleCrystal structure of Odorant Binding Protein 1 from Aedes albopictus (Asian tiger mosquito)
ComponentsOdorant-binding protein 1
KeywordsTRANSPORT PROTEIN / Odorant Binding Protein (OBP) / mosquito / olfaction / Carvacrol
Function / homology: / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / odorant binding / extracellular region / Odorant-binding protein 1
Function and homology information
Biological speciesAedes albopictus (Asian tiger mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiggri, P.G.V. / Tsitsanou, K.E. / Zographos, S.E.
Funding support Greece, 2items
OrganizationGrant numberCountry
Other governmentT1EDK-00996 Greece
Other governmentMIS5000432 Greece
CitationJournal: To Be Published
Title: Crystal structure of Odorant Binding Protein 1 from Aedes albopictus (Asian tiger mosquito)
Authors: Liggri, P.G.V. / Tsitsanou, K.E. / Zographos, S.E.
History
DepositionDec 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Odorant-binding protein 1


Theoretical massNumber of molelcules
Total (without water)14,1901
Polymers14,1901
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.337, 81.337, 63.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

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Components

#1: Protein Odorant-binding protein 1 / Putative odorant binding protein


Mass: 14190.069 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes albopictus (Asian tiger mosquito)
Gene: 109422789, RP20_CCG014341, RP20_CCG027709 / Production host: Escherichia coli (E. coli) / References: UniProt: H9A9Y0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1.6M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2→47.35 Å / Num. obs: 16836 / % possible obs: 99.96 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.072 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.65 / Num. unique obs: 1662 / CC1/2: 0.94 / % possible all: 99.82

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OG0

6og0


Resolution: 2→47.35 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.561 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19749 829 4.9 %RANDOM
Rwork0.164 ---
obs0.16559 16002 99.95 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.683 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å2-0 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 0 58 1050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0181034
X-RAY DIFFRACTIONr_bond_other_d0.0010.02956
X-RAY DIFFRACTIONr_angle_refined_deg1.291.8691397
X-RAY DIFFRACTIONr_angle_other_deg1.1652.7932215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5555125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0824.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76715193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.456155
X-RAY DIFFRACTIONr_chiral_restr0.0770.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_mcbond_it7.6752.432497
X-RAY DIFFRACTIONr_mcbond_other7.4432.424496
X-RAY DIFFRACTIONr_mcangle_it7.9793.565623
X-RAY DIFFRACTIONr_mcangle_other7.9863.581624
X-RAY DIFFRACTIONr_scbond_it15.3623.385537
X-RAY DIFFRACTIONr_scbond_other15.2643.353534
X-RAY DIFFRACTIONr_scangle_other15.834.563773
X-RAY DIFFRACTIONr_long_range_B_refined15.19629.6291187
X-RAY DIFFRACTIONr_long_range_B_other15.2629.6261185
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 47 -
Rwork0.196 1170 -
obs--99.84 %
Refinement TLS params.Method: refined / Origin x: 26.774 Å / Origin y: -26.389 Å / Origin z: 5.905 Å
111213212223313233
T0.0112 Å2-0.0067 Å2-0.0029 Å2-0.0399 Å20.0127 Å2--0.0335 Å2
L2.5179 °20.5451 °2-0.404 °2-2.0955 °2-0.8393 °2--2.8799 °2
S-0.0144 Å °0.0346 Å °0.0549 Å °-0.0337 Å °0.062 Å °0.0712 Å °0.0124 Å °-0.2622 Å °-0.0476 Å °

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