8ZDE | pdb_00008zde

Crystal structure of HsmR with DNA bound

• PDB DOI: https://doi.org/10.2210/pdb8ZDE/pdb
• NAKB: 8ZDE

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


• Deposited: 2024-05-02 Released: 2025-11-05 
• Deposition Author(s): Park, S.Y.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 
  0.276 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of C. difficile HsmR with DNA bound

Park, S.Y., Rho, S.H.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 156.73 kDa 
• Atom Count: 9,524 
• Modeled Residue Count: 967 
• Deposited Residue Count: 1,134 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MarR-family transcriptional regulator	A, B, C, D, E, F	167	Clostridioides difficile	Mutation(s): 0  Gene Names: CDR20291_0782
UniProt
Find proteins for A0A9R0BIW1 (Clostridioides difficile (strain R20291)) Explore A0A9R0BIW1  Go to UniProtKB:  A0A9R0BIW1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*GP*TP*TP*TP*GP*TP*AP*TP*GP*CP*AP*AP*AP*CP*CP*AP*TP*T)-3')	G, I, K	22	Clostridioides difficile

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*GP*GP*TP*TP*TP*GP*CP*AP*TP*AP*CP*AP*AP*AP*CP*TP*AP*AP*T)-3')	H, J, L	22	Clostridioides difficile

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	M [auth G], N [auth J]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free:  0.276 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 262.113	α = 90
b = 55.705	β = 101.35
c = 117.525	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Park, S.Y.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2025-11-19
  Changes: Derived calculations