5X6D

Crystal structure of PrfA-DNA binary complex

• PDB DOI: https://doi.org/10.2210/pdb5X6D/pdb
• NAKB: 5X6D

• Classification: DNA BINDING PROTEN/DNA
• Organism(s): Listeria monocytogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-21 Released: 2017-04-12 
• Deposition Author(s): Wang, Y., Feng, H., Zhu, Y.L., Gao, P.
• Funding Organization(s): National Natural Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 0.266 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Structural insights into glutathione-mediated activation of the master regulator PrfA in Listeria monocytogenes

Wang, Y., Feng, H., Zhu, Y., Gao, P.

(2017) Protein Cell 8: 308-312

• PubMed: 28271443 
• DOI: https://doi.org/10.1007/s13238-017-0390-x
• Primary Citation of Related Structures:  
  5X6D, 5X6E

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Organizational Affiliation: 

Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

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 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 217.45 kDa 
• Atom Count: 15,015 
• Modelled Residue Count: 1,586 
• Deposited Residue Count: 1,596 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Listeriolysin positive regulatory factor A	A, B, E [auth G], F [auth H], I [auth M], J [auth N]	237	Listeria monocytogenes	Mutation(s): 0  Gene Names: prfA, AJL40_05990, AJN46_04535, M643_11230
UniProt
Find proteins for P22262 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore P22262  Go to UniProtKB:  P22262

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (29-MER)	C, H [auth K], L [auth P]	29	Listeria monocytogenes

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	D, G [auth L], K [auth O]	29	Listeria monocytogenes

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 0.266 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.82	α = 90
b = 96.443	β = 90
c = 371.911	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Wang, Y., Feng, H., Zhu, Y.L., Gao, P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation	China	31670903

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description