3DSB

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb3DSB/pdb

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


• Deposited: 2008-07-11 Released: 2008-09-09 
• Deposition Author(s): Tan, K., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

The crystal structure of a possible acetyltransferase from Clostridium difficile 630

Tan, K., Shackelford, G., Joachimiak, A.

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.79 kDa 
• Atom Count: 3,103 
• Modelled Residue Count: 304 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative acetyltransferase	A, B	157	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD2162
UniProt
Find proteins for Q185U9 (Clostridioides difficile (strain 630)) Explore Q185U9  Go to UniProtKB:  Q185U9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BET	D [auth A], F [auth B]	TRIMETHYL GLYCINE C5 H12 N O2 KWIUHFFTVRNATP-UHFFFAOYSA-O
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.205 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.488	α = 90
b = 66.765	β = 90
c = 133.884	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Tan, K., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations