4MMK | pdb_00004mmk

Q8A Hfq from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb4MMK/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: 2.16 Å
R-Value Free:
0.256 (Depositor), 0.194 (DCC)
R-Value Work:
0.216 (Depositor), 0.187 (DCC)
R-Value Observed:
0.229 (Depositor)

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

PubMed: 24954598 Search on PubMed
DOI: https://doi.org/10.1134/S0006297914050113
Primary Citation 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: 110.67 kDa
Atom Count: 6,928
Modeled Residue Count: 826
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein hfq	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HUM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth H] MOL2 format, chain IA [auth H] mmCIF format, chain IA [auth H]	IA [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth H] Interactions & Density Focus chain IA [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain GA [auth H] SDF format, chain HA [auth H] SDF format, chain JA [auth I] SDF format, chain KA [auth I] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth J] SDF format, chain P [auth B] SDF format, chain PA [auth K] SDF format, chain Q [auth B] SDF format, chain QA [auth K] SDF format, chain S [auth C] SDF format, chain SA [auth L] SDF format, chain T [auth C] SDF format, chain TA [auth L] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain JA [auth I] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth K] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain SA [auth L] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain GA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain JA [auth I] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth K] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain SA [auth L] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	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		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain PA [auth K] Focus chain Q [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain SA [auth L] Focus chain T [auth C] Focus chain TA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain PA [auth K] Focus chain Q [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain SA [auth L] Focus chain T [auth C] Focus chain TA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain MA [auth I] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain UA [auth L] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain MA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth L] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain DA [auth F] mmCIF format, chain MA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth L] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	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		Interactions Focus chain DA [auth F] Focus chain MA [auth I] Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain UA [auth L] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth F] Focus chain MA [auth I] Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain UA [auth L] Focus chain V [auth C] Focus chain Y [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain OA [auth J] SDF format, chain RA [auth K] MOL2 format, chain FA [auth G] MOL2 format, chain OA [auth J] MOL2 format, chain RA [auth K] mmCIF format, chain FA [auth G] mmCIF format, chain OA [auth J] mmCIF format, chain RA [auth K]	FA [auth G], OA [auth J], RA [auth K]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain OA [auth J] Focus chain RA [auth K] Interactions & Density Focus chain FA [auth G] Focus chain OA [auth J] Focus chain RA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.256 (Depositor), 0.194 (DCC)
R-Value Work: 0.216 (Depositor), 0.187 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.59	α = 90
b = 116.54	β = 119.98
c = 66.62	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
PHASER	phasing
PHENIX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

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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