2D4I

Monoclinic hen egg-white lysozyme crystallized at pH4.5 form heavy water solution

Structural Biology Knowledgebase: 2D4I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.136

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2D4I

Classification: HYDROLASE

Total Structure Weight: 28995.42

Macromolecule Entities
Molecule Chains Length Organism Details
Lysozyme C A, B 129 Gallus gallus EC#: 3.2.1.17 IUBMB
Gene Name(s): LYZ Gene View

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NO3
Query on NO3

A, B NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DOD
Query on DOD

A, B DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.175
  • R-Value Work: 0.136
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 28.01 α = 90.00
b = 62.92 β = 90.55
c = 60.49 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-20
  • Released Date: 2006-07-11
  • Deposition author(s): Harata, K., Akiba, T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update