4NY6

Neutron structure of leucine and valine methyl protonated type III antifreeze

• PDB DOI: https://doi.org/10.2210/pdb4NY6/pdb

• Classification: ANTIFREEZE PROTEIN
• Organism(s): Zoarces americanus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-12-10 Released: 2014-12-24 
• Deposition Author(s): Fisher, S.J., Blakeley, M.P., Howard, E.I., Petite-Haertlein, I., Haertlein, M., Mitschler, A., Cousido-Siah, A., Salvaya, A.G., Popov, A., Muller-Dieckmann, C., Petrova, T., Podjarny, A.D.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

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• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography.

Fisher, S.J., Blakeley, M.P., Howard, E.I., Petit-Haertlein, I., Haertlein, M., Mitschler, A., Cousido-Siah, A., Salvay, A.G., Popov, A., Muller-Dieckmann, C., Petrova, T., Podjarny, A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 3266-3272

• PubMed: 25478844 
• DOI: https://doi.org/10.1107/S1399004714021610
• Primary Citation of Related Structures:  
  4NY6


• PubMed Abstract: 
  

  The 1.8 Å resolution neutron structure of deuterated type III antifreeze protein in which the methyl groups of leucine and valine residues are selectively protonated is presented. Comparison between this and the 1.85 Å resolution neutron structure of perdeuterated type III antifreeze protein indicates that perdeuteration improves the visibility of solvent molecules located in close vicinity to hydrophobic residues, as cancellation effects between H atoms of the methyl groups and nearby heavy-water molecules (D2O) are avoided.

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Organizational Affiliation: 

Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France.

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: 6.89 kDa 
• Atom Count: 584 
• Modelled Residue Count: 65 
• Deposited Residue Count: 65 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type-3 ice-structuring protein HPLC 12	A	65	Zoarces americanus	Mutation(s): 0
UniProt
Find proteins for P19614 (Zoarces americanus) Explore P19614  Go to UniProtKB:  P19614

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.73	α = 90
b = 39.12	β = 90
c = 46.54	γ = 90

Software Package:

Software Name	Purpose
QLD	data collection
PHENIX	model building
PHENIX	refinement
LAUEGEN	data reduction
LSCALE	data scaling
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Fisher, S.J., Blakeley, M.P., Howard, E.I., Petite-Haertlein, I., Haertlein, M., Mitschler, A., Cousido-Siah, A., Salvaya, A.G., Popov, A., Muller-Dieckmann, C., Petrova, T., Podjarny, A.D.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-06-13
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Refinement description