3FES | pdb_00003fes

Crystal Structure of the ATP-dependent Clp Protease ClpC from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb3FES/pdb

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


• Deposited: 2008-12-01 Released: 2008-12-16 
• Deposition Author(s): Kim, Y., Tesar, C., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal Structure of the ATP-dependent Clp Protease ClpC from Clostridium difficile

Kim, Y., Tesar, C., Li, H., Cobb, G., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 65.33 kDa 
• Atom Count: 4,833 
• Modeled Residue Count: 565 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp endopeptidase	A, B, C, D	145	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD0026, clpC, mecB
UniProt
Find proteins for Q18CA9 (Clostridioides difficile (strain 630)) Explore Q18CA9  Go to UniProtKB:  Q18CA9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	H [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4	F [auth B], I [auth C], J [auth C], L [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	E [auth A], G [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.222 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.69	α = 66.91
b = 68.523	β = 86.23
c = 81.339	γ = 85.33

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-16 
Deposition Author(s): Kim, Y., Tesar, C., Li, H., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-12-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-11-06
  Changes: Structure summary