6LB3 | pdb_00006lb3

Crystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb6LB3/pdb
• NAKB: 6LB3

• Classification: ANTITOXIN/DNA
• Organism(s): Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-13 Released: 2020-11-18 
• Deposition Author(s): Liu, Y., Zhang, H., Gao, Z., Dong, Y.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas aeruginosa

Liu, Y., Zhang, H., Gao, Z., Dong, Y.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 131.15 kDa 
• Atom Count: 7,646 
• Modeled Residue Count: 821 
• Deposited Residue Count: 980 
• 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, E, F, G, H	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 (5'-D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3')	I, K, M	18	Pseudomonas aeruginosa

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3')	J, L, N	18	Pseudomonas aeruginosa

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	O [auth A], P [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.284	α = 90
b = 95.57	β = 96.29
c = 128.857	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Liu, Y., Zhang, H., Gao, Z., Dong, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	U1732113

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description