4MML

D40A Hfq from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb4MML/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-09-09 Released: 2014-07-09 
• Deposition Author(s): Murina, V.N., Filimonov, V.V., Melnik, B.S., Uhlein, M., Mueller, U., Weiss, M., Nikulin, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.164 
• R-Value Observed: 0.172 

Literature

Effect of conserved intersubunit amino Acid substitutions on hfq protein structure and stability.

Murina, V.N., Melnik, B.S., Filimonov, V.V., Uhlein, M., Weiss, M.S., Muller, U., Nikulin, A.D.

(2014) Biochemistry (Mosc) 79: 469-477

• PubMed: 24954598 
• DOI: https://doi.org/10.1134/S0006297914050113
• Primary Citation of Related Structures:  
  4MMK, 4MML


• PubMed Abstract: 
  

  Hfq is a thermostable RNA-binding bacterial protein that forms a uniquely shaped homohexamer. Based on sequence and structural similarity, Hfq belongs to the like-Sm (LSm) protein family. In spite of a rather high degree of homology between archaeal and eukaryotic LSm proteins, their quaternary structure is different, usually consisting of five to eight monomers. In this work, the importance of conserved intersubunit hydrogen bonds for the Hfq spatial organization was tested. The structures and stabilities for the Gln8Ala, Asn28Ala, Asp40Ala, and Tyr55Ala Hfq mutants were determined. All these proteins have the same hexamer organization, but their stability is different. Elimination of a single intersubunit hydrogen bond due to Gln8Ala, Asp40Ala, and Tyr55Ala substitutions results in decreased stability of the Hfq hexamer. Tyr55Ala Hfq as well as the earlier studied His57Ala Hfq has reduced protein thermostability, which seems to correspond to an opening of the protein hydrophobic core.

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Organizational Affiliation: 

Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 9.52 kDa 
• Atom Count: 586 
• Modelled Residue Count: 67 
• Deposited Residue Count: 82 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein hfq	A	82	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: hfq, PA4944
UniProt
Find proteins for Q9HUM0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUM0  Go to UniProtKB:  Q9HUM0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U	D [auth A]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.164 
• R-Value Observed: 0.172 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.79	α = 90
b = 65.79	β = 90
c = 28.13	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
PROCESS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Murina, V.N., Filimonov, V.V., Melnik, B.S., Uhlein, M., Mueller, U., Weiss, M., Nikulin, A.D.

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description