6Q03

Crystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine)

• PDB DOI: https://doi.org/10.2210/pdb6Q03/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-01 Released: 2019-11-27 
• Deposition Author(s): Dopkins, B.J., Call, C.J., Thoden, J.B., Holden, H.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of MurA from Clostridium difficile in the presence of UDP-N-acetyl-alpha-D-muramic acid with modified Cys116 (S-[(1S)-1-carboxy-1-(phosphonooxy)ethyl]-L-cysteine)

Dopkins, B.J., Call, C.J., Thoden, J.B., Holden, H.M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.87 kDa 
• Atom Count: 3,543 
• Modelled Residue Count: 416 
• Deposited Residue Count: 421 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 1-carboxyvinyltransferase	A	421	Clostridioides difficile 630	Mutation(s): 0  Gene Names: murA, CD630_01230 EC: 2.5.1.7
UniProt
Find proteins for Q18CL1 (Clostridioides difficile (strain 630)) Explore Q18CL1  Go to UniProtKB:  Q18CL1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPZ	B [auth A]	(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid C20 H31 N3 O19 P2 NQBRVZNDBBMBLJ-MQTLHLSBSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
QPA	A	L-PEPTIDE LINKING	C6 H12 N O8 P S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.946	α = 90
b = 138.946	β = 90
c = 138.946	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SAINT	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-27 
Deposition Author(s): Dopkins, B.J., Call, C.J., Thoden, J.B., Holden, H.M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115921

Revision History  

• Version 1.0: 2019-11-27
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary