3N9A | pdb_00003n9a

Mite-y Lysozyme: Vegemite

• PDB DOI: https://doi.org/10.2210/pdb3N9A/pdb

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


• Deposited: 2010-05-28 Released: 2011-06-08 
• Deposition Author(s): Newman, J., Peat, T.S., Lucent, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.189 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Mite-y Lysozyme Crystals and Structures

Newman, J., Peat, T.S., Lucent, D.

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: 14.37 kDa 
• Atom Count: 1,215 
• 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.189 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.289	α = 90
b = 79.289	β = 90
c = 37.889	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Newman, J., Peat, T.S., Lucent, D.

Revision History  

• Version 1.0: 2011-06-08
  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: 2024-10-16
  Changes: Structure summary