Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14731.63 
• Atom Count: 1029 
• Residue Count: 130 
• Unique protein chains: 1

1B7S

VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES

• DOI: 10.2210/pdb1B7S/pdb

• Classification: MUTANT STABILITY
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): 1 


• Deposited: 1999-01-25 Released: 1999-02-02 
• Deposition Author(s): Takano, K., Ota, M., Ogasahara, K., Yamagata, Y., Nishikawa, K., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.188 

Literature

Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes.

Takano, K., Ota, M., Ogasahara, K., Yamagata, Y., Nishikawa, K., Yutani, K.

(1999) Protein Eng. 12: 663-672

• PubMed: 10469827 
• Primary Citation of Related Structures:  
  1B7R, 1B7Q, 1B7P, 1B7O, 1B7M, 1B7N, 1B7L


• PubMed Abstract: 
  

The stability profile of mutant protein (SPMP) (Ota,M., Kanaya,S. and Nishikawa,K., 1995, J. Mol. Biol., 248, 733-738) estimates the changes in conformational stability due to single amino acid substitutions using a pseudo-energy potential developed for evaluating structure-sequence compatibility in the structure prediction method, the 3D-1D compatibility evaluation. Nine mutant human lysozymes expected to significantly increase in stability from SPMP were constructed, in order to experimentally verify the reliability of SPMP. The thermodynamic parameters for denaturation and crystal structures of these mutant proteins were determined. One mutant protein was stabilized as expected, compared with the wild-type protein. However, the others were not stabilized even though the structural changes were subtle, indicating that SPMP overestimates the increase in stability or underestimates negative effects due to substitution. The stability changes in the other mutant human lysozymes previously reported were also analyzed by SPMP. The correlation of the stability changes between the experiment and prediction depended on the types of substitution: there were some correlations for proline mutants and cavity-creating mutants, but no correlation for mutants related to side-chain hydrogen bonds. The present results may indicate some additional factors that should be considered in the calculation of SPMP, suggesting that SPMP can be refined further.

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Related Citations: 

• A General Rule for the Relationship between Hydrophobic Effect and Conformational Stability of a Protein: Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozyme
  Takano, K.,Yamagata, Y.,Yutani, K.
  (1998) J.Mol.Biol. 280: 749
• Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants
  Takano, K.,Yamagata, Y.,Fujii, S.,Yutani, K.
  (1997) Biochemistry 36: 688
• Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants
  Takano, K.,Ogasahara, K.,Kaneda, H.,Yamagata, Y.,Fujii, S.,Kanaya, E.,Kikuchi, M.,Oobatake, M.,Yutani, K.
  (1995) J.Mol.Biol. 254: 62
• Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine--> Phenylalanine Mutants
  Yamagata, Y.,Kubota, M.,Sumikawa, Y.,Funahashi, J.,Takano, K.,Fujii, S.,Yutani, K.
  (1998) Biochemistry 37: 9355
• Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability
  Takano, K.,Funahashi, J.,Yamagata, Y.,Fujii, S.,Yutani, K.
  (1997) J.Mol.Biol. 274: 132




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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME	A	130	Homo sapiens	Mutation(s): 1  Gene Names: LYZ (LZM) EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to Gene View: LYZ Go to UniProtKB:  P61626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.490	α = 90.00
b = 62.010	β = 90.00
c = 32.010	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-25 
• Released Date: 1999-02-02 
• Deposition Author(s): Takano, K., Ota, M., Ogasahara, K., Yamagata, Y., Nishikawa, K., Yutani, K.

Revision History 

• Version 1.0: 1999-02-02
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance