1DPW

STRUCTURE OF HEN EGG-WHITE LYSOZYME IN COMPLEX WITH MPD

• PDB DOI: https://doi.org/10.2210/pdb1DPW/pdb

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


• Deposited: 1999-12-28 Released: 2000-01-03 
• Deposition Author(s): Weiss, M.S., Palm, G.J., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.222 
• R-Value Work: 0.178 

Literature

Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD.

Weiss, M.S., Palm, G.J., Hilgenfeld, R.

(2000) Acta Crystallogr D Biol Crystallogr 56: 952-958

• PubMed: 10944331 
• DOI: https://doi.org/10.1107/s0907444900006685
• Primary Citation of Related Structures:  
  1DPW, 1DPX


• PubMed Abstract: 
  

  Hen egg-white lysozyme has been crystallized at slightly alkaline pH using 2-methyl-2,4-pentanediol (MPD) as the precipitant. The crystals are nearly isomorphous to crystals grown at acidic pH using sodium chloride as the precipitant. However, the growth kinetics differ markedly between the two conditions. The major reason for this is a molecule of MPD that binds tightly in between two lysozyme molecules and favors the growth of the crystals along the crystallographic c direction over growth perpendicular to it.

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Organizational Affiliation: 

Institute of Molecular Biotechnology, Department of Structural Biology and Crystallography, PO Box 100813, D-07708 Jena, 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: 14.76 kDa 
• Atom Count: 1,156 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A], E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MRD	F [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.222 
• R-Value Work: 0.178 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.51	α = 90
b = 77.51	β = 90
c = 37.42	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-03 
Deposition Author(s): Weiss, M.S., Palm, G.J., Hilgenfeld, R.

Revision History  

• Version 1.0: 2000-01-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-23
  Changes: Other