5JMU | pdb_00005jmu

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

• PDB DOI: https://doi.org/10.2210/pdb5JMU/pdb

• Classification: HYDROLASE
• Organism(s): Agathobacter rectalis ATCC 33656
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-29 Released: 2016-06-29 
• Deposition Author(s): Tan, K., Gu, M., Clancy, S., Joachimiak, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.189 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

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

Tan, K., Gu, M., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.22 kDa 
• Atom Count: 1,946 
• Modeled Residue Count: 220 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan N-acetylglucosamine deacetylase	A	226	Agathobacter rectalis ATCC 33656	Mutation(s): 0  Gene Names: EUBREC_2389
UniProt
Find proteins for C4ZEZ9 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZEZ9  Go to UniProtKB:  C4ZEZ9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
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 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.495	α = 90
b = 60.323	β = 90
c = 79.577	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	phasing
HKL-3000	data reduction
SBC-Collect	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

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

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary