1HC0

structure of lysozyme with periodate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Regular Arrangement of Periodates Bound to Lysozyme.

Ondracek, J.Weiss, M.S.Brynda, J.Fiala, J.Jursik, F.Rezacova, P.Jenner, L.B.Sedlacek, J.

(2005) Acta Crystallogr.,Sect.D 61: 1181

  • DOI: 10.1107/S090744490501543X

  • PubMed Abstract: 
  • The structure of tetragonal hen egg-white lysozyme soaked in a periodate solution has been determined to a resolution of 1.8 A. Four high-occupancy periodate positions have been identified on the basis of the anomalous signal of the I atoms. The four ...

    The structure of tetragonal hen egg-white lysozyme soaked in a periodate solution has been determined to a resolution of 1.8 A. Four high-occupancy periodate positions have been identified on the basis of the anomalous signal of the I atoms. The four periodates exhibit a regular rectangular arrangement on the surface of the lysozyme molecule. No similar regular arrangement was found either in lysozyme crystals soaked in other heavy-atom anions or in other structures from the Protein Data Bank. Depending on their position on the surface of the protein, the periodate ions deviate to a varying extent from ideal octahedral geometry.


    Organizational Affiliation

    Department of Recombinant Expression and Structural Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo n. 2, CZ-16637 Praha 6, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.765α = 90.00
b = 77.765β = 90.00
c = 37.555γ = 90.00
Software Package:
Software NamePurpose
HKLdata scaling
SHELXL-97refinement
HKL1998data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-14
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2016-12-14
    Type: Data collection, Other
  • Version 1.3: 2017-06-28
    Type: Data collection