5X6D | pdb_00005x6d

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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.266 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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 Related Structures: 
  5X6D, 5X6E

---

Organizational Affiliation: 
• Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Key Laboratory of Infection and Immunity, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

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 
• Modeled 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 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

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.

---

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