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.

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

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.0 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

PubMed: 24954598 Search on PubMed
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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HUM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U5P Query on U5P Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	URIDINE-5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₉ P DJJCXFVJDGTHFX-XVFCMESISA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

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
Version 2.0: 2024-10-16
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary