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- PDB-1a3y: ODORANT BINDING PROTEIN FROM NASAL MUCOSA OF PIG -

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Basic information

Entry
Database: PDB / ID: 1a3y
TitleODORANT BINDING PROTEIN FROM NASAL MUCOSA OF PIG
ComponentsODORANT BINDING PROTEIN
KeywordsLIPOCALIN / OLFACTION
Function / homology
Function and homology information


odorant binding / small molecule binding / sensory perception of smell / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Odorant-binding protein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSpinelli, S. / Cambillau, C. / Tegoni, M.
Citation
Journal: Biochemistry / Year: 1998
Title: The structure of the monomeric porcine odorant binding protein sheds light on the domain swapping mechanism.
Authors: Spinelli, S. / Ramoni, R. / Grolli, S. / Bonicel, J. / Cambillau, C. / Tegoni, M.
#1: Journal: Chem.Senses / Year: 1995
Title: Affinities of Nutty and Green-Smelling Pyrazines and Thiazoles to Odorant-Binding Proteins, in Relation with Their Lipophilicity
Authors: Herent, M.F. / Collin, S. / Pelosi, P.
#2: Journal: Chem.Senses / Year: 1993
Title: Binding of Selected Odorant to Bovine and Porcine Odorant-Binding Proteins
Authors: Monte, M.D. / Centini, M. / Anselmi, C. / Pelosi, P.
#3: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 1991
Title: Purification and Characterization of Two Odorant-Binding Proteins from Nasal Tissue of Rabbit and Pig
Authors: Dal Monte, M. / Andreini, I. / Revoltella, R. / Pelosi, P.
History
DepositionJan 27, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ODORANT BINDING PROTEIN
B: ODORANT BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,5392
Polymers33,5392
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.360, 88.730, 93.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ODORANT BINDING PROTEIN


Mass: 16769.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: NOSE / Tissue: OLFACTORY EPITHELIUM / References: UniProt: P81245
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
35 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 11000 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rsym value: 0.051 / Net I/σ(I): 12
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.265 / % possible all: 99
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OBP

1obp


Resolution: 2.25→25 Å / Rfactor Rfree error: 0.0002 / Data cutoff high absF: 10000000 / Data cutoff low absF: 100 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1295 6 %RANDOM
Rwork0.181 ---
obs0.181 21750 70 %-
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 197 2525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.25→2.37 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.28 25 11 %
Rwork0.18 200 -
obs--60 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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