8OFD | pdb_00008ofd

Crystal structure of beta-conglutin from Lupinus albus refined to 2.81 A

PDB DOI: https://doi.org/10.2210/pdb8OFD/pdb

Classification: ALLERGEN
Organism(s): Lupinus albus
Mutation(s): Yes

Deposited: 2023-03-15 Released: 2023-06-14
Deposition Author(s): Dolot, R.M., O'Sullivan, C.K., Jauset-Rubio, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.277 (Depositor), 0.314 (DCC)
R-Value Work:
0.204 (Depositor), 0.230 (DCC)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

First crystal structure of beta-conglutin, a major lupin allergen from Lupinus albus seeds

Dolot, R.M., O'Sullivan, C.K., Jauset-Rubio, M.

To be published.

Macromolecule Content

Total Structure Weight: 49.15 kDa
Atom Count: 3,387
Modeled Residue Count: 401
Deposited Residue Count: 423
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conglutin beta 1	A	423	Lupinus albus	Mutation(s): 1
UniProt
Find proteins for Q53HY0 (Lupinus albus) Explore Q53HY0 Go to UniProtKB: Q53HY0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53HY0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free: 0.277 (Depositor), 0.314 (DCC)
R-Value Work: 0.204 (Depositor), 0.230 (DCC)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.63	α = 90
b = 166.63	β = 90
c = 40.098	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

O'Sullivan, C.K.

Jauset-Rubio, M.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.