4X2D | pdb_00004x2d

Clostridium difficile Fic protein_0569 mutant S31A, E35A in complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb4X2D/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Clostridioides difficile R20291
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2014-11-26 Released: 2015-12-23 
• Deposition Author(s): Jorgensen, R., Dedic, E.
• Funding Organization(s): Danish Council for Independent Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Structure of Clostridium difficile Fic_0569 S31A, E35A mutant at 1.8 Angstroms resolution

Jorgensen, R., Dedic, E., Alsarraf, H., Welner, D., van Leeuwen, H.C., Oestergaard, O.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 109.72 kDa 
• Atom Count: 6,789 
• Modeled Residue Count: 831 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fic family protein putative filamentation induced by cAMP protein	A, B, C, D	235	Clostridioides difficile R20291	Mutation(s): 2  Gene Names: CDR20291_0569

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.08	α = 90
b = 60.1	β = 118.6
c = 124.83	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Jorgensen, R., Dedic, E.

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Funding Organization	Location	Grant Number
Danish Council for Independent Research	Denmark	11-104831/FSS

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Refinement description