1F10

CRYSTAL STRUCTURE OF ORTHORHOMBIC LYSOZYME GROWN AT PH 6.5 AT 88% RELATIVE HUMIDITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 

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This is version 1.2 of the entry. See complete history

Literature

Hydration, mobility and accessibility of lysozyme: structures of a pH 6.5 orthorhombic form and its low-humidity variant and a comparative study involving 20 crystallographically independent molecules.

Biswal, B.K.Sukumar, N.Vijayan, M.

(2000) Acta Crystallogr.,Sect.D 56: 1110-1119

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure analyses of orthorhombic lysozyme grown at pH 6.5 and its low-humidity variant are reported. The structures of the same form grown at pH 9.5 and 4.5 and that of the low-humidity variant of the pH 9.5 form are available. A comparison bet ...

    The structure analyses of orthorhombic lysozyme grown at pH 6.5 and its low-humidity variant are reported. The structures of the same form grown at pH 9.5 and 4.5 and that of the low-humidity variant of the pH 9.5 form are available. A comparison between them shows that the changes in molecular geometry and hydration caused by changes in the amount of solvent surrounding protein molecules are more pronounced than those caused by variation in pH. In particular, the conformation and the mutual orientation of the catalytic residues Glu35 and Asp52 remain unaffected by change in pH. A comparative study involving 20 crystallographically independent lysozyme molecules, including five in the orthorhombic form, leads to the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. Half the binding cleft (subsites D, E and F) belong to the rigid region but the other half (subsites A, B and C) belong to a flexible region. There is no marked correlation between relative rigidity and conservation of side-chain conformation except at the binding site. The study permits the identification of seven invariant water molecules associated with the protein. Most of them are involved in important tertiary interactions, while one occurs in the active-site cleft. The study demonstrates a weak correlation between non-accessibility and rigidity. On average, the level of hydration of polar atoms increases rapidly with accessible atomic surface area, but levels off at about 15 A(2) at a little over one ordered water molecule per polar protein atom. Only 15 N and O atoms are hydrated in all 20 molecules. 13 of these are hydrated by the seven invariant water molecules. Of the seven, only one water molecule is totally buried within the protein.


    Related Citations: 
    • Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
      Madhusudan,Kodandapani, R.,Vijayan, M.
      (1993) Acta Crystallogr.,Sect.D 49: 234
    • Structures of Orthorhombic Lysozyme Grown at Basic pH and its Low-Humidity Variant
      Sukumar, N.,Biswal, B.K.,Vijayan, M.
      (1999) Acta Crystallogr.,Sect.D 55: 934
    • Crystal Structure of Low Humidity Tetragonal Lysozyme at 2.1-A Resolution. Variability in Hydration Shell and its Structural Consequences
      Kodandapani, R.,Suresh, C.G.,Vijayan, M.
      (1990) J.Biol.Chem. 265: 16126


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.584α = 90.00
b = 55.859β = 90.00
c = 68.583γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
XDSdata reduction
XDSdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-06-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance