Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.87 kDa 
• Atom Count: 1540 
• Residue Count: 178 
• Unique protein chains: 1

1XJT

Crystal structure of active form of P1 phage endolysin Lyz

• DOI: 10.2210/pdb1XJT/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia virus P1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-09-24 Released: 2005-01-11 
• Deposition Author(s): Arockiasamy, A., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme.

Xu, M., Arulandu, A., Struck, D.K., Swanson, S., Sacchettini, J.C., Young, R.

(2005) Science 307: 113-117

• PubMed: 15637279 
• DOI: 10.1126/science.1105143
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-disulfide isomerization, which requires a cysteine in its N-terminal SAR (signal-arrest-release) domain. Crystal structures confirm the alternative disulfide linkages in the two forms of Lyz and reveal dramatic conformational differences in the catalytic domain. Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	A	191	Escherichia virus P1	Mutation(s): 8  Gene Names: 17, lysa, lyz EC: 3.2.1.17
Find proteins for Q37875 (Escherichia phage P1) Go to UniProtKB:  Q37875

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	A	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.871	α = 90
b = 66.871	β = 90
c = 166.796	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Adxv	data processing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-24 
• Released Date: 2005-01-11 
Deposition Author(s): Arockiasamy, A., Sacchettini, J.C.

Revision History 

• Version 1.0: 2005-01-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description