3A34 | pdb_00003a34

Effect of Ariginine on lysozyme

• PDB DOI: https://doi.org/10.2210/pdb3A34/pdb

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


• Deposited: 2009-06-09 Released: 2010-06-16 
• Deposition Author(s): Ito, L., Shiraki, K., Matsuura, T., Yamaguchi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Implication of Arg bindings on aromatic surfaces of lysozyme for additives that prevent protein aggregation

Ito, L., Shiraki, K., Matsuura, T., Yamaguchi, H.

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: 15.22 kDa 
• Atom Count: 1,200 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	B [auth A], C [auth A], D [auth A], E [auth A]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O
ACT	J [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.357	α = 90
b = 78.357	β = 90
c = 37.312	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Ito, L., Shiraki, K., Matsuura, T., Yamaguchi, H.

Revision History  

• Version 1.0: 2010-06-16
  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: 2024-10-30
  Changes: Structure summary