1IWW

Crystal Structure Analysis of Human lysozyme at 152K.


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1107/S0907444902011277
  • Primary Citation of Related Structures:  
    1IWT, 1IWU, 1IWV, 1IWW, 1IWX, 1IWY, 1IWZ

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LYSOZYME CA130Homo sapiensMutation(s): 0 
Gene Names: LYZLZM
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
GTEx:  ENSG00000090382 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61626
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 56.286α = 90
b = 61.121β = 90
c = 33.099γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
NMREFrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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