3FE9 | pdb_00003fe9

Crystal structure of a pheromone binding protein from Apis mellifera with a serendipitous ligand soaked at pH 7.0

• PDB DOI: https://doi.org/10.2210/pdb3FE9/pdb

• Classification: Pheromone binding protein
• Organism(s): Apis mellifera
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2008-11-28 Released: 2009-12-01 
• Deposition Author(s): Pesenti, M.E., Spinelli, S., Bezirard, V., Briand, L., Pernollet, J.C., Tegoni, M., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.187 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Queen bee pheromone binding protein pH induced domain-swapping favors pheromone release

Pesenti, M.E., Spinelli, S., Bezirard, V., Briand, L., Pernollet, J.C., Tegoni, M., Cambillau, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.84 kDa 
• Atom Count: 1,137 
• Modeled Residue Count: 117 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pheromone-binding protein ASP1	A	119	Apis mellifera	Mutation(s): 0
UniProt
Find proteins for Q9U9J6 (Apis mellifera) Explore Q9U9J6  Go to UniProtKB:  Q9U9J6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMJ	B [auth A]	(20S)-20-methyldotetracontane C43 H88 RQRQHJNVHOWJHC-QLKFWGTOSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.187 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.298	α = 90
b = 83.909	β = 90
c = 46.804	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Pesenti, M.E., Spinelli, S., Bezirard, V., Briand, L., Pernollet, J.C., Tegoni, M., Cambillau, C.

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary