Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 24.90 kDa 
• Atom Count: 1135 
• Modelled Residue Count: 129 
• Deposited Residue Count: 213 
• Unique protein chains: 1

1O5L

Crystal structure of Transcriptional regulator (TM1171) from Thermotoga maritima at 2.30 A resolution

• PDB DOI: 10.2210/pdb1O5L/pdb

• Classification: TRANSCRIPTION
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-23 Released: 2003-10-07 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171.

Spraggon, G., Pantazatos, D., Klock, H.E., Wilson, I.A., Woods, V.L., Lesley, S.A.

(2004) Protein Sci 13: 3187-3199

• PubMed: 15557262 
• DOI: 10.1110/ps.04939904
• Primary Citation of Related Structures:  
  1O5L, 1SJ5, 1VJL


• PubMed Abstract: 
  

The structure of two Thermotoga maritima proteins, a conserved hypothetical protein (TM0160) and a transcriptional regulator (TM1171), have now been determined at 1.9 A and 2.3 A resolution, respectively, as part of a large-scale structural genomics project. Our first efforts to crystallize full-length versions of these targets were unsuccessful. However, analysis of the recombinant purified proteins using the technique of enhanced amide hydrogen/deuterium exchange mass spectroscopy (DXMS) revealed substantial regions of rapid amide deuterium hydrogen exchange, consistent with flexible regions of the structures. Based on these exchange data, truncations were designed to selectively remove the disordered C-terminal regions, and the resulting daughter proteins showed greatly enhanced crystallizability. Comparative DXMS analysis of full-length protein versus truncated forms demonstrated complete and exact preservation of the exchange rate profiles in the retained sequence, indicative of conservation of the native folded structure. This study presents the first structures produced with the aid of the DXMS method for salvaging intractable crystallization targets. The structure of TM0160 represents a new fold and highlights the use of this approach where any prior structural knowledge is absent. The structure of TM1171 represents an example where the lack of a substrate/cofactor may impair crystallization. The details of both structures are presented and discussed.

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Organizational Affiliation: 

Joint Center for Structural Genomics, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcriptional regulator, crp family	A	213	Thermotoga maritima	Mutation(s): 0  Gene Names: TM1171
UniProt
Find proteins for Q9X0Q3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0Q3  Go to UniProtKB:  Q9X0Q3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.971	α = 90
b = 62.971	β = 90
c = 167.103	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-23 
• Released Date: 2003-10-07 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2003-10-07
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2018-07-18
  Changes: Data collection, Database references