Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.69 kDa 
• Atom Count: 1258 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

1GE3

CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME SUBSTITUTED AT LEFT-HANDED HELICAL POSITIONS

• PDB DOI: 10.2210/pdb1GE3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2000-10-06 Released: 2000-11-08 
• Deposition Author(s): Takano, K., Yamagata, Y., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.190 

Literature

Role of non-glycine residues in left-handed helical conformation for the conformational stability of human lysozyme

Takano, K., Yamagata, Y., Yutani, K.

(2001) Proteins 44: 233-243

• PubMed: 11455596 
• DOI: 10.1002/prot.1088
• Primary Citation of Related Structures:  
  1GDW, 1GDX, 1GE0, 1GE1, 1GE2, 1GE3, 1GE4


• PubMed Abstract: 
  

To understand the role of non-Gly residues in the left-handed helical conformation for the conformational stability of a protein, the non-Gly to Gly and Ala mutations at six left-handed residues (R21, Y38, R50, Q58, H78, and N118) of the human lysozyme were examined. The thermodynamic parameters for denaturation were determined using a differential scanning calorimeter, and the crystal structures were analyzed by X-ray crystallography. If a left-handed non-Gly had an unfavorable steric interaction between the side-chain Cbeta and backbone, the Gly mutation would be expected to stabilize more than the Ala mutation at the same position. For the mutant human lysozymes, however, there were few differences in the denaturation Gibbs energy (DeltaG) between the Gly and Ala mutants, except for the substitution at position 58. Analysis of the changes in stability (DeltaDeltaG) based on the structures of the wild-type and mutant proteins showed that the experimental DeltaDeltaG value of Q58G was approximately 7 kJ/mol higher than the estimated value without consideration of any local steric interaction. These results indicate that only Q58G increased the stability by elimination of local constraints. The residue 58 is located at the most rigid position in the left-handed non-Gly residues and is involved in its enzymatic function. It can be concluded that the left-handed non-Gly residues do not always have unfavorable strain energies as compared with Gly at the same position.

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Related Citations: 

• Role of Amino Acid Residues at Turns in the Conformational Stability and Folding of Human Lysozyme
  Takano, K., Yamagata, Y., Yutani, K.
  (2000) Biochemistry 39: 8655

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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME C	A	130	Homo sapiens	Mutation(s): 1  Gene Names: LYZ, LZM EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens) Explore P61626  Go to UniProtKB:  P61626
PHAROS:  P61626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 60.67	β = 90
c = 32.96	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-10-06 
• Released Date: 2000-11-08 
Deposition Author(s): Takano, K., Yamagata, Y., Yutani, K.

Revision History  

• Version 1.0: 2000-11-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations