3HDE | pdb_00003hde

Crystal structure of full-length endolysin R21 from phage 21

• PDB DOI: https://doi.org/10.2210/pdb3HDE/pdb

• Classification: HYDROLASE
• Organism(s): Enterobacteria phage P21
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2009-05-07 Released: 2009-11-03 
• Deposition Author(s): Sun, Q., Arockiasamy, A., McKee, E., Caronna, E., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 

Literature

Regulation of a muralytic enzyme by dynamic membrane topology.

Sun, Q., Kuty, G.F., Arockiasamy, A., Xu, M., Young, R., Sacchettini, J.C.

(2009) Nat Struct Mol Biol 16: 1192-1194

• PubMed: 19881499 
• DOI: https://doi.org/10.1038/nsmb.1681
• Primary Citation Related Structures: 
  3HDE, 3HDF


• PubMed Abstract: 
  

  R(21), the lysozyme of coliphage 21, has an N-terminal signal-anchor-release (SAR) domain that directs its secretion in a membrane-tethered, inactive form and then its release and activation in the periplasm. Both genetic and crystallographic studies show that the SAR domain, once extracted from the bilayer, refolds into the body of the enzyme and effects muralytic activation by repositioning one residue of the canonical lysozyme catalytic triad.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.16 kDa 
• Atom Count: 5,281 
• Modeled Residue Count: 651 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A, B, C, D	165	Enterobacteria phage P21	Mutation(s): 0  Gene Names: R EC: 3.2.1.17 Membrane Entity: Yes
UniProt
Find proteins for P27359 (Enterobacteria phage P21) Explore P27359  Go to UniProtKB:  P27359

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.249	α = 90
b = 94.814	β = 90
c = 97.65	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Sun, Q., Arockiasamy, A., McKee, E., Caronna, E., Sacchettini, J.C.

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Structure summary