2HUB | pdb_00002hub

Structure of Hen Egg-White Lysozyme Determined from crystals grown in pH 7.5

• PDB DOI: https://doi.org/10.2210/pdb2HUB/pdb

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


• Deposited: 2006-07-26 Released: 2007-07-24 
• Deposition Author(s): Frolow, F., Lagziel-Simis, S., Cohen-Hadar, N., Wine, Y., Freeman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: other

Literature

Monitoring influence of pH on the molecular and crystal structure of hen egg-white tetragonal lysozyme

Lagziel-Simis, S., Wine, Y., Cohen-Hadar, N., Freeman, A., Frolow, F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.92 kDa 
• Atom Count: 1,269 
• Modeled 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
TAR	F [auth A]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N
PPI	E [auth A]	PROPANOIC ACID C3 H6 O2 XBDQKXXYIPTUBI-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.861	α = 90
b = 76.861	β = 90
c = 35.867	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Frolow, F., Lagziel-Simis, S., Cohen-Hadar, N., Wine, Y., Freeman, A.

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.4: 2024-04-03
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary