5X6E | pdb_00005x6e

Crystal structure of PrfA-DNA binary complex

• PDB DOI: https://doi.org/10.2210/pdb5X6E/pdb
• NAKB: 5X6E

• Classification: DNA BINDING PROTEIN/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

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

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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.
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 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: 219.3 kDa 
• Atom Count: 15,154 
• Modeled Residue Count: 1,588 
• 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 [auth M], B [auth N], E [auth A], F [auth B], I [auth E], J [auth F]	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 [auth O], G [auth C], K [auth G]	29	Listeria monocytogenes

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	M, N, O [auth A], P [auth B], Q [auth E], R [auth F]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	M, N, O [auth A], P [auth B], Q [auth E], R [auth F]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.300 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.017	α = 90
b = 96.59	β = 90
c = 370.528	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references