Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14.83 kDa 
• Atom Count: 2416 
• Residue Count: 130 
• Unique protein chains: 1

1IWW

Crystal Structure Analysis of Human lysozyme at 152K.

• DOI: 10.2210/pdb1IWW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2002-06-03 Released: 2002-09-04 
• Deposition Author(s): Joti, Y., Nakasako, M., Kidera, A., Go, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.190 
• R-Value Work: 0.168 

Literature

Nonlinear temperature dependence of the crystal structure of lysozyme: correlation between coordinate shifts and thermal factors.

Joti, Y., Nakasako, M., Kidera, A., Go, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1421-1432

• PubMed: 12198298 
• DOI: 10.1107/S0907444902011277
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The static and dynamic structures of human lysozyme at seven different temperatures ranging from 113 to 178 K were investigated by normal-mode refinement of the cryogenic X-ray diffraction data collected from a single crystal. Normal-mode refinement decomposes the mean-square fluctuations of protein atoms from their average position into the contributions from the internal degrees of freedom, which change the shape of the protein structure, and those from the external degrees of freedom, which generate rigid-body motions in the crystal. While at temperatures below 150 K the temperature dependence of the total mean-square fluctuations shows a small gradient similar to that predicted theoretically by normal-mode analysis, at temperatures above 150 K there is an apparent inflection in the temperature dependence with a higher gradient. The inflection in the temperature dependence at temperatures above 150 K occurs mostly in the external degrees of freedom. Possible causes for the dynamic transition are discussed with respect to the crystal packing and physicochemical properties of crystalline water.

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Organizational Affiliation: 

Department of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME C	A	130	Homo sapiens	Mutation(s): 0  Gene Names: LYZ, LZM EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS  P61626 GTEx  ENSG00000090382

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.190 
• R-Value Work: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.286	α = 90
b = 61.121	β = 90
c = 33.099	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
NMREF	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-03 
• Released Date: 2002-09-04 
Deposition Author(s): Joti, Y., Nakasako, M., Kidera, A., Go, N.

Revision History 

• Version 1.0: 2002-09-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance