7T8I | pdb_00007t8i

Crystal structure of the ImmR transcriptional regulator DNA-binding domain of Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.346 (Depositor), 0.346 (DCC) 
  • R-Value Work: 
    0.259 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure report of the ImmR transcriptional regulator DNA-binding domain of the Bacillus subtilis ICEBs1 transposon.

Caliandro, R.de Diego, I.Gomis-Ruth, F.X.

(2022) Sci Rep 12: 5258-5258

  • DOI: https://doi.org/10.1038/s41598-022-09237-2
  • Primary Citation Related Structures: 
    7T8I

  • PubMed Abstract: 

    Bacillus subtilis is a commensal member of the human oral and gut microbiomes, which can become infectious to immunocompromised patients. It possesses a conjugative transposon, ICEBs1, which includes > 20 genes and can be passed by horizontal gene transfer to other bacteria, including pathogenic Bacillus anthracis and Listeria monocytogenes. ICEBs1 is regulated by the ImmR/ImmA tandem, which are a transcriptional repressor that constitutively blocks transcription and a metallopeptidase that acts as anti-repressor and inactivates ImmR by proteolytic cleavage. We here report the production and purification of 127-residue ImmR from ICEBs1 and the crystal structure of its DNA-binding domain. It features a five-helix bundle centred on a helix-turn-helix motif potentially binding the major grove of double-stranded target DNA. ImmR shows structural and mechanistic similarity with the B. subtilis SinR repressor, which is engaged in sporulation inhibition.


  • Organizational Affiliation
    • Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park, C/Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain.

Macromolecule Content 

  • Total Structure Weight: 15 kDa 
  • Atom Count: 1,202 
  • Modeled Residue Count: 130 
  • Deposited Residue Count: 132 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage element (ICEBs1)transcriptional regulator (Xre family)66Bacillus subtilisMutation(s): 0 
Gene Names: B4417_4397SC09_Contig25orf00616
UniProt
Find proteins for P96631 (Bacillus subtilis (strain 168))
Explore P96631 
Go to UniProtKB:  P96631
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96631
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage element (ICEBs1)transcriptional regulator (Xre family)66Bacillus subtilisMutation(s): 0 
Gene Names: B4417_4397SC09_Contig25orf00616
UniProt
Find proteins for P96631 (Bacillus subtilis (strain 168))
Explore P96631 
Go to UniProtKB:  P96631
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP96631
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
A
L-PEPTIDE LINKINGC7 H16 N2 O2LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.346 (Depositor), 0.346 (DCC) 
  • R-Value Work:  0.259 (Depositor), 0.259 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.033α = 90
b = 48.34β = 97.474
c = 64.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHASERphasing
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-03-30
    Changes: Database references, Structure summary
  • Version 1.2: 2022-04-06
    Changes: Database references
  • Version 1.3: 2022-04-13
    Changes: Database references
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description