3AJN | pdb_00003ajn

Structural basis of glycine amide on suppression of protein aggregation by high resolution X-ray analysis

• PDB DOI: https://doi.org/10.2210/pdb3AJN/pdb
• Entry: 3AJN supersedes: 2ZXS

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2010-06-09 Released: 2011-02-16 
• Deposition Author(s): Ito, L., Shiraki, K., Hasegawa, K., Kumasaka, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

Glycine amide shielding on the aromatic surfaces of lysozyme: Implication for suppression of protein aggregation

Ito, L., Shiraki, K., Makino, M., Hasegawa, K., Kumasaka, T.

(2011) FEBS Lett 585: 555-560

• PubMed: 21237160 
• DOI: https://doi.org/10.1016/j.febslet.2011.01.008
• Primary Citation Related Structures: 
  3AJN


• PubMed Abstract: 
  

  Glycine amide (GlyAd), a typically amidated amino acid, is a versatile additive that suppresses protein aggregation during refolding, heat treatment, and crystallization. In spite of its effectiveness, the exact mechanism by which GlyAd suppresses protein aggregation remains to be elucidated. Here, we show the crystal structure of the GlyAd-lysozyme complex by high resolution X-ray crystallographic analysis at a 1.05Å resolution. GlyAd bound to the lysozyme surface near aromatic residues and decreased the amount of bound waters and increased the mobility of protein. Arg and GlyAd molecules are different in binding sites and patterns from glycerol and related compounds, indicating that decreasing hydrophobic patches might be involved in suppression of protein aggregation.

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Organizational Affiliation: 
• Japan Synchrotron Radiation Research Institute (SPring-8), Sayo, Hyogo, Japan. [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: 14.72 kDa 
• Atom Count: 1,285 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GM1	B [auth A], C [auth A], D [auth A], E [auth A]	AMINOMETHYLAMIDE C2 H6 N2 O BEBCJVAWIBVWNZ-UHFFFAOYSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.51	α = 90
b = 78.51	β = 90
c = 36.962	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-16 
Deposition Author(s): Ito, L., Shiraki, K., Hasegawa, K., Kumasaka, T.
• This entry supersedes: 2ZXS

Revision History  

• Version 1.0: 2011-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary