3IPJ

The crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb3IPJ/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-08-17 Released: 2009-10-20 
• Deposition Author(s): Zhang, R., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.170 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 

Literature

The crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile

Zhang, R., Bigelow, L., 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)

Macromolecule Content

• Total Structure Weight: 21.7 kDa 
• Atom Count: 1,767 
• Modelled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system, IIabc component	A, B	95	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD0469, GI:115249482
UniProt
Find proteins for Q188R0 (Clostridioides difficile (strain 630)) Explore Q188R0  Go to UniProtKB:  Q188R0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.170 
• R-Value Work: 0.133 
• R-Value Observed: 0.135 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.635	α = 90
b = 34.734	β = 90.07
c = 72.195	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Zhang, R., Bigelow, L., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations