4IDL

Low melting temperature Anti-Cholera Toxin Llama VHH domain

• PDB DOI: https://doi.org/10.2210/pdb4IDL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-12-12 Released: 2013-02-13 
• Deposition Author(s): Legler, P.M., Lam, A., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Structure of a low-melting-temperature anti-cholera toxin: llama V(H)H domain.

Legler, P.M., Zabetakis, D., Anderson, G.P., Lam, A., Hol, W.G., Goldman, E.R.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 90-93

• PubMed: 23385744 
• DOI: https://doi.org/10.1107/S1744309112050750
• Primary Citation of Related Structures:  
  4IDL


• PubMed Abstract: 
  

  Variable heavy domains derived from the heavy-chain-only antibodies found in camelids (V(H)H domains) are known for their thermal stability. Here, the structure of A9, an anti-cholera toxin V(H)H domain (K(d) = 77 ± 5 nM) that has an unusually low melting temperature of 319.9 ± 1.6 K, is reported. The CDR3 residues of A9 form a β-hairpin that is directed away from the former V(H)-V(L) interfacial surface, exposing hydrophobic residues to the solvent. A DALI structural similarity search showed that this CDR3 conformation is uncommon.

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Organizational Affiliation: 

Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA. [e-mail]

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: 14.9 kDa 
• Atom Count: 1,000 
• Modelled Residue Count: 123 
• Deposited Residue Count: 136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single Domain Antibody VHH A9	A	136	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.444	α = 90
b = 51.863	β = 107.81
c = 46.481	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Legler, P.M., Lam, A., Hol, W.G.J.

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary