3ONM | pdb_00003onm

Effector binding Domain of LysR-Type transcription factor RovM from Y. pseudotuberculosis

• PDB DOI: https://doi.org/10.2210/pdb3ONM/pdb

• Classification: TRANSCRIPTION
• Organism(s): Yersinia pseudotuberculosis IP 31758
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-30 Released: 2011-01-26 
• Deposition Author(s): Quade, N., Diekmann, M., Haffke, M., Heroven, A.K., Dersch, P., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.295 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Structure of the effector-binding domain of the LysR-type transcription factor RovM from Yersinia pseudotuberculosis.

Quade, N., Dieckmann, M., Haffke, M., Heroven, A.K., Dersch, P., Heinz, D.W.

(2011) Acta Crystallogr D Biol Crystallogr 67: 81-90

• PubMed: 21245528 
• DOI: https://doi.org/10.1107/S0907444910049681
• Primary Citation Related Structures: 
  3ONM


• PubMed Abstract: 
  

  In enteropathogenic Yersinia, the expression of several early-phase virulence factors such as invasin is tightly regulated in response to environmental cues. The responsible regulatory network is complex, involving several regulatory RNAs and proteins such as the LysR-type transcription regulator (LTTR) RovM. In this study, the crystal structure of the effector-binding domain (EBD) of RovM, the first LTTR protein described as being involved in virulence regulation, was determined at a resolution of 2.4 Å. Size-exclusion chromatography and comparison with structures of full-length LTTRs show that RovM is most likely to adopt a tetrameric arrangement with two distant DNA-binding domains (DBDs), causing the DNA to bend around it. Additionally, a cavity was detected in RovM which could bind small inducer molecules.

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Organizational Affiliation: 
• Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.32 kDa 
• Atom Count: 2,857 
• Modeled Residue Count: 370 
• Deposited Residue Count: 476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator LrhA	A, B	238	Yersinia pseudotuberculosis IP 31758	Mutation(s): 0  Gene Names: lrhA, RovM, YpsIP31758_1452

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.295 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.468	α = 90
b = 69.468	β = 90
c = 351.216	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Quade, N., Diekmann, M., Haffke, M., Heroven, A.K., Dersch, P., Heinz, D.W.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references