148L

A COVALENT ENZYME-SUBSTRATE INTERMEDIATE WITH SACCHARIDE DISTORTION IN A MUTANT T4 LYSOZYME

• PDB DOI: https://doi.org/10.2210/pdb148L/pdb

• Classification: HYDROLASE/HYDROLASE SUBSTRATE
• Organism(s): Tequatrovirus T4, Escherichia coli
• Mutation(s): No 


• Deposited: 1993-10-27 Released: 1994-04-30 
• Deposition Author(s): Kuroki, R., Weaver, L.H., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.168 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.69 kDa 
• Atom Count: 1,525 
• Modelled Residue Count: 167 
• Deposited Residue Count: 168 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T4 LYSOZYME	A [auth E]	164	Tequatrovirus T4	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SUBSTRATE CLEAVED FROM CELL WALL OF ESCHERICHIA COLI	B [auth S]	4	Escherichia coli	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid	C [auth A]	2		N/A
Glycosylation Resources
GlyTouCan:  G88499BX GlyCosmos:  G88499BX

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BME	D [auth E]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
API	B [auth S]	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.9	α = 90
b = 67.3	β = 90
c = 49.6	γ = 90

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-04-30 
Deposition Author(s): Kuroki, R., Weaver, L.H., Matthews, B.W.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary