2FBB

Crystal Structure Analysis of Hexagonal Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb2FBB/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2005-12-09 Released: 2006-03-28 
• Deposition Author(s): Brinkmann, C., Weiss, M.S., Weckert, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.198 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

The structure of the hexagonal crystal form of hen egg-white lysozyme.

Brinkmann, C., Weiss, M.S., Weckert, E.

(2006) Acta Crystallogr D Biol Crystallogr 62: 349-355

• PubMed: 16552135 
• DOI: https://doi.org/10.1107/S0907444906000825
• Primary Citation of Related Structures:  
  2FBB


• PubMed Abstract: 
  

  The three-dimensional structure of hen egg-white lysozyme (HEWL) in a hexagonal crystal form has been determined and refined to 1.46 A resolution. This hexagonal crystal form crystallizes from a saturated sodium nitrate solution at pH 8.4. The crystals belong to space group P6(1)22, with unit-cell parameters a = b = 85.64, c = 67.93 A. A total of 165 water molecules, 16 nitrate ions and five sodium ions were located in the electron-density map. The hexagonal crystal form exhibits a higher solvent content and a higher degree of disorder than other crystal forms of lysozyme. The flexibility of the protein depends on the crystal packing, although some residue ranges are flexible in all native HEWL crystal forms.

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Organizational Affiliation: 

HASYLAB at DESY, Notkestrasse 85, 22607 Hamburg, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.44 kDa 
• Atom Count: 1,252 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.198 
• R-Value Work: 0.183 
• R-Value Observed: 0.183 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.637	α = 90
b = 85.637	β = 90
c = 67.932	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-28 
Deposition Author(s): Brinkmann, C., Weiss, M.S., Weckert, E.

Revision History  

• Version 1.0: 2006-03-28
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description