6YOA

Lig v 1 structure and the inflammatory response to the Ole e 1 protein family

• PDB DOI: https://doi.org/10.2210/pdb6YOA/pdb

• Classification: ALLERGEN
• Organism(s): Ligustrum vulgare
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2020-04-14 Released: 2020-05-13 
• Deposition Author(s): Robledo-Retana, T., Bradley-Clark, J., Croll, T., Rose, R., Stagg, A., Villalba, M., Pickersgill, R.
• Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.319 
• R-Value Work: 0.262 
• R-Value Observed: 0.265 

Starting Model: experimental

Literature

Lig v 1 structure and the inflammatory response to the Ole e 1 protein family.

Robledo Retana, T., Bradley-Clarke, J., Croll, T., Rose, R., Hoti, I., Stagg, A.J., Villalba, M., Pickersgill, R.W.

(2020) Allergy 75: 2395-2398

• PubMed: 32359174 
• DOI: https://doi.org/10.1111/all.14351
• Primary Citation of Related Structures:  
  6YOA

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Organizational Affiliation: 

Department of Biochemistry, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.02 kDa 
• Atom Count: 2,194 
• Modelled Residue Count: 275 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major pollen allergen Lig v 1	A, B	145	Ligustrum vulgare	Mutation(s): 0
UniProt
Find proteins for O82015 (Ligustrum vulgare) Explore O82015  Go to UniProtKB:  O82015

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 0.319 
• R-Value Work: 0.262 
• R-Value Observed: 0.265 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.484	α = 90
b = 76.484	β = 90
c = 113.498	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Robledo-Retana, T., Bradley-Clark, J., Croll, T., Rose, R., Stagg, A., Villalba, M., Pickersgill, R.

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Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	409358
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary