5FMN | pdb_00005fmn

The nickel-responsive transcriptional regulator InrS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.282 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5FMN

This is version 1.4 of the entry. See complete history

Literature

A tight tunable range for Ni(II) sensing and buffering in cells.

Foster, A.W.Pernil, R.Patterson, C.J.Scott, A.J.Palsson, L.O.Pal, R.Cummins, I.Chivers, P.T.Pohl, E.Robinson, N.J.

(2017) Nat Chem Biol 13: 409-414

  • DOI: https://doi.org/10.1038/nchembio.2310
  • Primary Citation Related Structures: 
    5FMN

  • PubMed Abstract: 

    The metal affinities of metal-sensing transcriptional regulators co-vary with cellular metal concentrations over more than 12 orders of magnitude. To understand the cause of this relationship, we determined the structure of the Ni(II) sensor InrS and then created cyanobacteria (Synechocystis PCC 6803) in which transcription of genes encoding a Ni(II) exporter and a Ni(II) importer were controlled by InrS variants with weaker Ni(II) affinities. Variant strains were sensitive to elevated nickel and contained more nickel, but the increase was small compared with the change in Ni(II) affinity. All of the variant sensors retained the allosteric mechanism that inhibits DNA binding following metal binding, but a response to nickel in vivo was observed only when the sensitivity was set to respond in a relatively narrow (less than two orders of magnitude) range of nickel concentrations. Thus, the Ni(II) affinity of InrS is attuned to cellular metal concentrations rather than the converse.


  • Organizational Affiliation
    • Department of Biosciences, Durham University, DH1 3LE, UK.

Macromolecule Content 

  • Total Structure Weight: 24.08 kDa 
  • Atom Count: 1,431 
  • Modeled Residue Count: 175 
  • Deposited Residue Count: 214 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INRS
A, B
107Synechocystis sp. PCC 6803Mutation(s): 0 
UniProt
Find proteins for Q55554 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q55554 
Go to UniProtKB:  Q55554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55554
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.282 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.29α = 90
b = 77.79β = 90
c = 85.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 1.2: 2017-03-29
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Other