3IVP

The structure of a possible transposon-related DNA-binding protein from Clostridium difficile 630.

• PDB DOI: https://doi.org/10.2210/pdb3IVP/pdb

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


• Deposited: 2009-09-01 Released: 2009-09-22 
• Deposition Author(s): Tan, K., Marshall, N., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

The structure of a possible transposon-related DNA-binding protein from Clostridium difficile 630.

Tan, K., Marshall, N., Jedrzejczak, R., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.82 kDa 
• Atom Count: 3,805 
• Modelled Residue Count: 452 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transposon-related DNA-binding protein	A, B, C, D	126	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD3330, Clostridium difficile
UniProt
Find proteins for Q180H4 (Clostridioides difficile (strain 630)) Explore Q180H4  Go to UniProtKB:  Q180H4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth C], F [auth C], G [auth D]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-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: 2.02 Å
• R-Value Free: 0.235 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.326	α = 90
b = 69.829	β = 90
c = 170.359	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Tan, K., Marshall, N., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary