4NY6 | pdb_00004ny6

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.

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)

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

wwPDB Validation 3D Report Full Report

This is version 1.3 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 D Biol Crystallogr 70: 3266-3272

PubMed: 25478844 Search on PubMed
DOI: https://doi.org/10.1107/S1399004714021610
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 6.89 kDa
Atom Count: 584
Modeled Residue Count: 65
Deposited Residue Count: 65
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19614
Sequence Annotations Expand
Reference Sequence

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), 0.188 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (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

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Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Revision History (Full details and data files)

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