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- PDB-8aei: X-ray structure of Canis familiaris Odorant Binding Protein 2 bou... -

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Basic information

Entry
Database: PDB / ID: 8aei
TitleX-ray structure of Canis familiaris Odorant Binding Protein 2 bound to citronellal
ComponentsMinor allergen Can f 2
KeywordsTRANSPORT PROTEIN / Odorant binding protein
Function / homology
Function and homology information


small molecule binding / extracellular space
Similarity search - Function
Major urinary protein / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin signature.
Similarity search - Domain/homology
(3R)-3,7-dimethyloct-6-en-1-ol / Minor allergen Can f 2
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSchwartz, M. / Briand, L.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
CitationJournal: To Be Published
Title: Structure of dog odorant binding protein
Authors: Glaz, M. / Schwartz, M. / Briand, L.
History
DepositionJul 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor allergen Can f 2
B: Minor allergen Can f 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3096
Polymers39,9482
Non-polymers3614
Water3,045169
1
A: Minor allergen Can f 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1553
Polymers19,9741
Non-polymers1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Minor allergen Can f 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1553
Polymers19,9741
Non-polymers1812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.562, 48.685, 67.102
Angle α, β, γ (deg.)90.000, 105.197, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Minor allergen Can f 2 / Allergen Dog 2


Mass: 19974.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: O18874
#2: Chemical ChemComp-ODM / (3R)-3,7-dimethyloct-6-en-1-ol / citronellol


Mass: 156.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 35% PEG 4000, 0.2 M MgCl2 in 0.1 M pH 8.0 Tris buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978566 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978566 Å / Relative weight: 1
ReflectionResolution: 1.74→48.69 Å / Num. obs: 32275 / % possible obs: 97 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Net I/σ(I): 19
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.376 / Num. unique obs: 1535 / CC1/2: 0.949 / Rpim(I) all: 0.153 / Rrim(I) all: 0.407 / % possible all: 85

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L4R

3l4r


Resolution: 1.74→38.91 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5942
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2189 1575 4.88 %
Rwork0.1903 30676 -
obs0.1918 32251 96.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.9 Å2
Refinement stepCycle: LAST / Resolution: 1.74→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 24 169 2615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592496
X-RAY DIFFRACTIONf_angle_d0.8073373
X-RAY DIFFRACTIONf_chiral_restr0.0556365
X-RAY DIFFRACTIONf_plane_restr0.005440
X-RAY DIFFRACTIONf_dihedral_angle_d11.7597335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.32551080.2462569X-RAY DIFFRACTION89.23
1.79-1.860.25841510.20532739X-RAY DIFFRACTION96.3
1.86-1.930.24441350.19372794X-RAY DIFFRACTION96.6
1.93-2.020.2621470.18312768X-RAY DIFFRACTION96.88
2.02-2.120.18681460.17922774X-RAY DIFFRACTION97.14
2.13-2.260.21261520.18172803X-RAY DIFFRACTION97.43
2.26-2.430.24721460.20162819X-RAY DIFFRACTION97.53
2.43-2.680.24731500.20612820X-RAY DIFFRACTION98.05
2.68-3.060.24941480.20742827X-RAY DIFFRACTION97.7
3.06-3.860.22281450.17682837X-RAY DIFFRACTION98.29
3.86-38.910.17651470.1842926X-RAY DIFFRACTION97.62

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