4NY6

Neutron structure of leucine and valine methyl protonated type III antifreeze


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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.,Sect.D 70: 3266-3272

  • DOI: 10.1107/S1399004714021610

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-3 ice-structuring protein HPLC 12
A
65Zoarces americanusMutation(s): 0 
Find proteins for P19614 (Zoarces americanus)
Go to UniProtKB:  P19614
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.730α = 90.00
b = 39.120β = 90.00
c = 46.540γ = 90.00
Software Package:
Software NamePurpose
QLDdata collection
PHENIXmodel building
LAUEGENdata reduction
LSCALEdata scaling
PHENIXphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description
  • Version 1.2: 2018-06-13
    Type: Data collection, Refinement description