9CU3 | pdb_00009cu3

Allosteric mechanism of DriD transcription activator

• PDB DOI: https://doi.org/10.2210/pdb9CU3/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Caulobacter vibrioides CB15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-25 Released: 2025-04-23 
• Deposition Author(s): Cannistraci, E.G., Schumacher, M.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Molecular mechanism of ssDNA-mediated allosteric activation of the C. crescentus WYL-domain containing transcription regulator, DriD

Cannistraci, E.G., Srinivasu, B.Y., Chavez Orozco Jr, J.C., Gozzi, K., Wales, T.E., Schumacher, M.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: gel filtration

Macromolecule Content 

• Total Structure Weight: 59.95 kDa 
• Atom Count: 3,719 
• Modeled Residue Count: 399 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WYL domain-containing protein	A [auth B], B [auth A]	271	Caulobacter vibrioides CB15	Mutation(s): 0  Gene Names: CC_1095
UniProt
Find proteins for Q9A999 (Caulobacter vibrioides (strain ATCC 19089 / CIP 103742 / CB 15)) Explore Q9A999  Go to UniProtKB:  Q9A999

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth B], E [auth B], F [auth B], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth B], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.231 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.796	α = 90
b = 88.796	β = 90
c = 141.523	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Cannistraci, E.G., Schumacher, M.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM130290

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release