4MMK

Q8A Hfq from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.229 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

    Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. thyrada@rambler.ru.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein hfq
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
82Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: hfqPA4944
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HUM0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IA [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth F]
CA [auth F]
EA [auth G]
GA [auth H]
AA [auth E],
BA [auth F],
CA [auth F],
EA [auth G],
GA [auth H],
HA [auth H],
JA [auth I],
KA [auth I],
LA [auth I],
M [auth A],
N [auth A],
NA [auth J],
P [auth B],
PA [auth K],
Q [auth B],
QA [auth K],
S [auth C],
SA [auth L],
T [auth C],
TA [auth L],
W [auth D],
X [auth D],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
DA [auth F]
MA [auth I]
O [auth A]
R [auth B]
U [auth C]
DA [auth F],
MA [auth I],
O [auth A],
R [auth B],
U [auth C],
UA [auth L],
V [auth C],
Y [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
FA [auth G],
OA [auth J],
RA [auth K]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.59α = 90
b = 116.54β = 119.98
c = 66.62γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
PHENIXrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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