1A3Y | pdb_00001a3y

ODORANT BINDING PROTEIN FROM NASAL MUCOSA OF PIG

• PDB DOI: https://doi.org/10.2210/pdb1A3Y/pdb

• Classification: LIPOCALIN
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 1998-01-27 Released: 1999-02-16 
• Deposition Author(s): Spinelli, S., Cambillau, C., Tegoni, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.181 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The structure of the monomeric porcine odorant binding protein sheds light on the domain swapping mechanism.

Spinelli, S., Ramoni, R., Grolli, S., Bonicel, J., Cambillau, C., Tegoni, M.

(1998) Biochemistry 37: 7913-7918

• PubMed: 9609684 
• DOI: https://doi.org/10.1021/bi980179e
• Primary Citation Related Structures: 
  1A3Y


• PubMed Abstract: 
  

  The X-ray structure of the porcine odorant binding protein (OBPp) was determined at 2.25 A resolution. This lipocalin is a monomer and is devoid of naturally occurring bound ligand, contrary to what was observed in the case of bovine OBP [Tegoni, M., et al. (1996) Nat. Struct. Biol. 3, 863-867; Bianchet, M. A., et al. (1996) Nat. Struct. Biol. 3, 934-939]. In this latter protein, a dimer without any disulfide bridges, domain swapping was found to occur between the beta- and alpha-domains. A single Gly (121) insertion was found in OBPp when it was compared to OBPb, which may prevent domain swapping from taking place. The presence of a disulfide bridge between the OBPp beta- and alpha-domains (cysteines 63 and 155) may lock the resulting fold in a nonswapped monomeric conformation. Comparisons with other OBPs indicate that the two cysteines involved in the OBPp disulfide bridge are conserved in the sequence, suggesting that OBPp may be considered a prototypic OBP fold, and not OBPb.

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Organizational Affiliation: 
• Architecture et Fonction des Macromolécules Biologiques, UPR 9039, CNRS, IFR1, Marseille, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.54 kDa 
• Atom Count: 2,515 
• Modeled Residue Count: 296 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ODORANT BINDING PROTEIN	A, B	149	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P81245 (Sus scrofa) Explore P81245  Go to UniProtKB:  P81245

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.181 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.36	α = 90
b = 88.73	β = 90
c = 93.19	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-16 
Deposition Author(s): Spinelli, S., Cambillau, C., Tegoni, M.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary