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- PDB-8aej: X-ray structure of Canis familiaris Odorant Binding Protein 3 bou... -

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Basic information

Entry
Database: PDB / ID: 8aej
TitleX-ray structure of Canis familiaris Odorant Binding Protein 3 bound to menthone
ComponentsLipocalin Can f 6.0101
KeywordsTRANSPORT PROTEIN / Odorant binding protein
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space / extracellular region
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
(+)-menthone / Lipocalin Can f 6.0101
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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
Revision 1.1Oct 23, 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

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Assembly

Deposited unit
A: Lipocalin Can f 6.0101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9472
Polymers21,7931
Non-polymers1541
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.075, 67.075, 71.985
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Lipocalin Can f 6.0101 / Allergen Can f 6


Mass: 21792.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: H2B3G5
#2: Chemical ChemComp-LWE / (+)-menthone


Mass: 154.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.15 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 550, 6% 2-propanol in 0.1 M pH 4.6 sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564 Å / Relative weight: 1
ReflectionResolution: 1.84→45.21 Å / Num. obs: 16710 / % possible obs: 99.8 % / Redundancy: 19.9 % / Biso Wilson estimate: 35.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.01 / Rrim(I) all: 0.035 / Net I/σ(I): 42
Reflection shellResolution: 1.84→1.88 Å / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 5.2 / Num. unique obs: 970 / CC1/2: 0.985 / Rpim(I) all: 0.105 / Rrim(I) all: 0.473

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NRE

6nre


Resolution: 1.84→45.21 Å / SU ML: 0.2386 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2439
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2608 881 5.29 %
Rwork0.2201 15780 -
obs0.2222 16661 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.64 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1304 0 11 62 1377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01171336
X-RAY DIFFRACTIONf_angle_d1.21921797
X-RAY DIFFRACTIONf_chiral_restr0.0725201
X-RAY DIFFRACTIONf_plane_restr0.007230
X-RAY DIFFRACTIONf_dihedral_angle_d21.3084514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.960.35691700.28512554X-RAY DIFFRACTION99.27
1.96-2.110.36021400.27442591X-RAY DIFFRACTION99.67
2.11-2.320.33881360.26512611X-RAY DIFFRACTION99.93
2.32-2.650.33131470.26592615X-RAY DIFFRACTION99.96
2.65-3.340.27761440.23672644X-RAY DIFFRACTION99.96
3.34-45.210.20511440.18392765X-RAY DIFFRACTION99.97

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