3FXR | pdb_00003fxr

Crystal structure of TsaR in complex with sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.269 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural studies on the full-length LysR-type regulator TsaR from Comamonas testosteroni T-2 reveal a novel open conformation of the tetrameric LTTR fold

Monferrer, D.Tralau, T.Kertesz, M.A.Dix, I.Sola, M.Uson, I.

(2010) Mol Microbiol 75: 1199-1214

  • DOI: https://doi.org/10.1111/j.1365-2958.2010.07043.x
  • Primary Citation Related Structures: 
    3FXQ, 3FXR, 3FXU, 3FZJ

  • PubMed Abstract: 

    LysR-type transcriptional regulators (LTTRs) constitute the largest family of regulators in prokaryotes. The full-length structures of the LTTR TsaR from Comamonas testosteroni T-2 and its complex with the natural inducer para-toluensulfonate have been characterized by X-ray diffraction. Both ligand-free and complexed forms reveal a dramatically different quaternary structure from that of CbnR from Ralstonia eutropha, or a putative LysR-type regulator from Pseudomonas aeruginosa, the only other determined full-length structures of tetrameric LTTRs. Although all three show a head-to-head tetrameric ring, TsaR displays an open conformation, whereas CbnR and PA01-PR present additional contacts in opposing C-terminal domains that close the ring. Such large differences may be due to a broader structural versatility than previously assumed or either, reflect the intrinsic flexibility of tetrameric LTTRs. On the grounds of the sliding dimer hypothesis of LTTR activation, we propose a structural model in which the closed structures could reflect the conformation of a ligand-free LTTR, whereas inducer binding would bring about local changes to disrupt the interface linking the two compact C-terminal domains. This could lead to a TsaR-like, open structure, where the pairs of recognition helices are closer to each other by more than 10 A.


  • Organizational Affiliation
    • IBMB-CSIC, Baldiri Reixach 15, Barcelona Science Park, 08028, Barcelona, Spain.

Macromolecule Content 

  • Total Structure Weight: 68.7 kDa 
  • Atom Count: 4,909 
  • Modeled Residue Count: 592 
  • Deposited Residue Count: 610 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LysR type regulator of tsaMBCD
A, B
305Comamonas testosteroniMutation(s): 0 
Gene Names: tsaR
UniProt
Find proteins for P94678 (Comamonas testosteroni)
Explore P94678 
Go to UniProtKB:  P94678
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94678
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ASC

Query on ASC



Download:Ideal Coordinates CCD File
K [auth A]ASCORBIC ACID
C6 H8 O6
CIWBSHSKHKDKBQ-JLAZNSOCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.269 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.11α = 90
b = 51.83β = 110.52
c = 107.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RESOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary