6JPI

Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6JPI/pdb
• NAKB: 6JPI

• Classification: ANTITOXIN/DNA
• Organism(s): Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-03-27 Released: 2020-04-01 
• Deposition Author(s): Liu, Y., Gao, Z., Zhang, H., Dong, Y.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.281 
• R-Value Work: 0.215 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Crystal structure of PA4674 in complex with its operator DNA (28bp) from Pseudomonas aeruginosa

Liu, Y., Gao, Z., Zhang, H., Dong, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 66.14 kDa 
• Atom Count: 4,073 
• Modelled Residue Count: 425 
• Deposited Residue Count: 492 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH cro/C1-type domain-containing protein	A, B, C, D	109	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA4674
UniProt
Find proteins for Q9HVC1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVC1  Go to UniProtKB:  Q9HVC1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	E	28	Pseudomonas aeruginosa

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (28-MER)	F	28	Pseudomonas aeruginosa

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.14 Å
• R-Value Free: 0.281 
• R-Value Work: 0.215 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.8	α = 90
b = 90.7	β = 90
c = 91.7	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Liu, Y., Gao, Z., Zhang, H., Dong, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	U1732113

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description