5JMU

The crystal structure of the catalytic domain of peptidoglycan N-acetylglucosamine deacetylase from Eubacterium rectale ATCC 33656


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 5JMU

Classification: HYDROLASE

Total Structure Weight: 25224.77

Macromolecule Entities
Molecule Chains Length Organism Details
Peptidoglycan N-acetylglucosamine deacetylase A 226 [eubacterium] rectale Fragment: catalytic domain (UNP residues 247-496)
Gene Name(s): EUBREC_2389
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET
OCS
Query on OCS
A L-PEPTIDE LINKING C3 H7 N O5 S CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.189
  • R-Value Work: 0.155
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 46.49 α = 90.00
b = 60.32 β = 90.00
c = 79.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-04-29
  • Released Date: 2016-06-29
  • Deposition author(s): Tan, K., Gu, M., Clancy, S., Joachimiak, A.

Revision History

  • Version 1_0: 2016-06-29

    Type: Initial release

  • Version 1_1: 2017-09-27

    Type: Author supporting evidence, Derived calculations