2WQL | pdb_00002wql

CRYSTAL STRUCTURE OF THE MAJOR CARROT ALLERGEN DAU C 1

PDB DOI: https://doi.org/10.2210/pdb2WQL/pdb
Entry: 2WQL supersedes: 2VJG

Classification: ALLERGEN
Organism(s): Daucus carota
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-08-24 Released: 2009-09-01
Deposition Author(s): Markovic-Housley, Z., Basle, A., Padavattan, S., Hoffmann-Sommergruber, K., Schirmer, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.221 (Depositor), 0.230 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of the Major Carrot Allergen Dau C 1.

Markovic-Housley, Z., Basle, A., Padavattan, S., Maderegger, B., Schirmer, T., Hoffmann-Sommergruber, K.

(2009) Acta Crystallogr D Biol Crystallogr 65: 1206

PubMed: 19923716 Search on PubMed
DOI: https://doi.org/10.1107/S0907444909034854
Primary Citation of Related Structures:
2WQL

PubMed Abstract:
Dau c 1 is a major allergen of carrot (Daucus carota) which displays IgE cross-reactivity with the homologous major birch-pollen allergen Bet v 1. The crystal structure of Dau c 1 has been determined to a resolution of 2.7 A, revealing tight dimers. The structure of Dau c 1 is similar to those of the major allergens from celery, Api g 1, and birch pollen, Bet v 1. Electron density has been observed in the hydrophobic cavity of each monomer and has been modelled with polyethylene glycol oligomers of varying length. Comparison of the surface topology and physicochemical properties of Dau c 1 and Bet v 1 revealed that they may have some, but not all, epitopes in common. This is in agreement with the observation that the majority of carrot-allergic patients have Bet v 1 cross-reactive IgE antibodies, whereas others have Dau c 1-specific IgE antibodies which do not recognize Bet v 1.

Organizational Affiliation

Core Program of Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland. zora.housley@unibas.ch

Macromolecule Content

Total Structure Weight: 66.84 kDa
Atom Count: 4,626
Modeled Residue Count: 608
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR ALLERGEN DAU C 1	A, B, C, D	154	Daucus carota	Mutation(s): 4
UniProt
Find proteins for O04298 (Daucus carota) Explore O04298 Go to UniProtKB: O04298
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O04298
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4C Query on P4C Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D]	E [auth A], K [auth B], S [auth C], Y [auth D]	O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL C₁₄ H₂₈ O₈ CTLLATPOKUEFSQ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain S [auth C] Focus chain Y [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D]	F [auth A] L [auth B] M [auth B] N [auth B] T [auth C] F [auth A], L [auth B], M [auth B], N [auth B], T [auth C], Z [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain R [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] mmCIF format, chain R [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] G [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.221 (Depositor), 0.230 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.948	α = 90
b = 189.948	β = 90
c = 189.948	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Markovic-Housley, Z.

Basle, A.

Padavattan, S.

Hoffmann-Sommergruber, K.

Schirmer, T.

This entry supersedes: 2VJG

Revision History (Full details and data files)

Version 1.0: 2009-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description