6YOA | pdb_00006yoa

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 (Depositor), 0.336 (DCC) 
• R-Value Work: 
  0.262 (Depositor), 0.276 (DCC) 
• R-Value Observed: 
  0.265 (Depositor) 

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 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.
Cambridge Institute for Medical Research, Cambridge, UK.
Protein Production Facility, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK.
Biochemistry and Molecular Biology I, Complutense University of Madrid Faculty of Chemical Sciences, Madrid, Spain.

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 
• Modeled 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 (Depositor), 0.336 (DCC) 
• R-Value Work:  0.262 (Depositor), 0.276 (DCC) 
• R-Value Observed: 0.265 (Depositor) 

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