1YS7 | pdb_00001ys7

Crystal structure of the response regulator protein prrA complexed with Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.230 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1YS7

This is version 1.5 of the entry. See complete history

Literature

The structural basis of signal transduction for the response regulator PrrA from Mycobacterium tuberculosis.

Nowak, E.Panjikar, S.Konarev, P.Svergun, D.I.Tucker, P.A.

(2006) J Biological Chem 281: 9659-9666

  • DOI: https://doi.org/10.1074/jbc.M512004200
  • Primary Citation Related Structures: 
    1YS7

  • PubMed Abstract: 

    The structure of the two-domain response regulator PrrA from Mycobacterium tuberculosis shows a compact structure in the crystal with a well defined interdomain interface. The interface, which does not include the interdomain linker, makes the recognition helix and the trans-activation loop of the effector domain inaccessible for interaction with DNA. Part of the interface involves hydrogen-bonding interactions of a tyrosine residue in the receiver domain that is believed to be involved in signal transduction, which, if disrupted, would destabilize the interdomain interface, allowing a more extended conformation of the molecule, which would in turn allow access to the recognition helix. In solution, there is evidence for an equilibrium between compact and extended forms of the protein that is far toward the compact form when the protein is inactivated but moves toward a more extended form when activated by the cognate sensor kinase PrrB.


  • Organizational Affiliation
    • European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 50.55 kDa 
  • Atom Count: 3,636 
  • Modeled Residue Count: 450 
  • Deposited Residue Count: 466 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulatory protein prrA
A, B
233Mycobacterium tuberculosisMutation(s): 0 
UniProt
Find proteins for P9WGM1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGM1 
Go to UniProtKB:  P9WGM1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGM1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
G [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.230 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.35α = 100.33
b = 46.486β = 102.01
c = 65.554γ = 92.9
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2016-12-21
    Changes: Structure summary
  • Version 1.4: 2016-12-28
    Changes: Database references
  • Version 1.5: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description