2Z2F | pdb_00002z2f

X-ray Crystal Structure of Bovine Stomach Lysozyme

• PDB DOI: https://doi.org/10.2210/pdb2Z2F/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2007-05-21 Released: 2008-05-27 
• Deposition Author(s): Akieda, D., Nonaka, Y., Watanabe, N., Tanaka, I., Kamiya, M., Aizawa, T., Nitta, K., Demura, M., Kawano, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.221 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Stability of Bovine Stomach Lysozyme in Acidic Condition

Akieda, D., Nonaka, Y., Watanabe, N., Tanaka, I., Kamiya, M., Aizawa, T., Nitta, K., Demura, M., Kawano, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.69 kDa 
• Atom Count: 1,278 
• 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-2	A	129	Bos taurus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for Q06283 (Bos taurus) Explore Q06283  Go to UniProtKB:  Q06283

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.221 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.257	α = 90
b = 56.065	β = 90
c = 64.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-27 
Deposition Author(s): Akieda, D., Nonaka, Y., Watanabe, N., Tanaka, I., Kamiya, M., Aizawa, T., Nitta, K., Demura, M., Kawano, K.

Revision History  

• Version 1.0: 2008-05-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-09
  Changes: Structure summary