2D4J

Transformed monoclinic crystal of hen egg-white lysozyme from a heavy water solution

Structural Biology Knowledgebase: 2D4J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 0.133
  • R-Value Work: 0.097

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2D4J

Classification: HYDROLASE

Total Structure Weight: 14579.26

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

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

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

A 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: 0.133
  • R-Value Work: 0.097
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 26.46 α = 90.00
b = 58.18 β = 111.33
c = 30.85 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: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4