2J8F

Crystal structure of the modular Cpl-1 endolysin complexed with a peptidoglycan analogue (E94Q mutant in complex with a disaccharide- pentapeptide)

• PDB DOI: https://doi.org/10.2210/pdb2J8F/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus phage Cp1
• Expression System: Escherichia coli DH1
• Mutation(s): Yes 


• Deposited: 2006-10-25 Released: 2007-07-03 
• Deposition Author(s): Perez-Dorado, I., Hermoso, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.215 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.61 kDa 
• Atom Count: 3,186 
• Modelled Residue Count: 338 
• Deposited Residue Count: 339 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME	A	339	Streptococcus phage Cp1	Mutation(s): 1  EC: 3.2.1.17
UniProt
Find proteins for P15057 (Streptococcus phage Cp-1) Explore P15057  Go to UniProtKB:  P15057

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G69619HL GlyCosmos:  G69619HL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGL	F [auth A]	D-GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-GSVOUGTGSA-N
ALA	D [auth A], E [auth A]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
FMT	G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.215 
• R-Value Work: 0.181 
• R-Value Observed: 0.181 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.23	α = 90
b = 95.59	β = 90
c = 129.27	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Perez-Dorado, I., Hermoso, J.A.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-04-10
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary