6Q11 | pdb_00006q11

Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID

• PDB DOI: https://doi.org/10.2210/pdb6Q11/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-08-02 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.226 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MurA from Clostridium difficile, mutation C116S, in the presence of URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID

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: 45.76 kDa 
• Atom Count: 3,480 
• Modeled 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): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPU	B [auth A]	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID C20 H29 N3 O19 P2 BEGZZYPUNCJHKP-DBYWSUQTSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.226 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.951	α = 90
b = 137.951	β = 90
c = 137.951	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
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.

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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, Derived calculations, Refinement description