7KD3 | pdb_00007kd3

Structure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291

• PDB DOI: https://doi.org/10.2210/pdb7KD3/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Clostridioides difficile R20291
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-07 Released: 2021-09-15 
• Deposition Author(s): Menon, S.K., Isom, C.E., Karr, E.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.258 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an HxlR/DUF24 family transcription regulator, CdTR_3200 from hypervirulent Clostridioides difficile R20291

Menon, S.K., Isom, C.E., West, A.H., Richter-Addo, G.B., Karr, E.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)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 26.41 kDa 
• Atom Count: 1,587 
• Modeled Residue Count: 197 
• Deposited Residue Count: 228 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	A	114	Clostridioides difficile R20291	Mutation(s): 0  Gene Names: CDR20291_3200

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator	B	114	Clostridioides difficile R20291	Mutation(s): 0  Gene Names: CDR20291_3200

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.258 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.019	α = 90
b = 55.001	β = 96.06
c = 72.317	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-15 
Deposition Author(s): Menon, S.K., Isom, C.E., Karr, E.A.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2021-09-15
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-23
  Changes: Structure summary