Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.07 kDa 
• Atom Count: 4084 
• Modelled Residue Count: 493 
• Deposited Residue Count: 498 
• Unique protein chains: 1

1MKM

CRYSTAL STRUCTURE OF THE THERMOTOGA MARITIMA ICLR

• PDB DOI: 10.2210/pdb1MKM/pdb
• Entry: 1MKM supersedes: 1JMR

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


• Deposited: 2002-08-29 Released: 2002-09-11 
• Deposition Author(s): Kim, Y., Zhang, R.G., Joachimiak, A., Skarina, T., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.300 
• R-Value Work: 0.232 
• R-Value Observed: 0.257 

Literature

Crystal structure of Thermotoga maritima 0065, a member of the IclR transcriptional factor family.

Zhang, R.G., Kim, Y., Skarina, T., Beasley, S., Laskowski, R., Arrowsmith, C., Edwards, A., Joachimiak, A., Savchenko, A.

(2002) J Biol Chem 277: 19183-19190

• PubMed: 11877432 
• DOI: 10.1074/jbc.M112171200
• Primary Citation of Related Structures:  
  1MKM


• PubMed Abstract: 
  

Members of the IclR family of transcription regulators modulate signal-dependent expression of genes involved in carbon metabolism in bacteria and archaea. The Thermotoga maritima TM0065 gene codes for a protein (TM-IclR) that is homologous to the IclR family. We have determined the crystal structure of TM-IclR at 2.2 A resolution using MAD phasing and synchrotron radiation. The protein is composed of two domains: the N-terminal DNA-binding domain contains the winged helix-turn-helix motif, and the C-terminal presumed regulatory domain is involved in binding signal molecule. In a proposed signal-binding site, a bound Zn(2+) ion was found. In the crystal, TM-IclR forms a dimer through interactions between DNA-binding domains. In the dimer, the DNA-binding domains are 2-fold related, but the dimer is asymmetric with respect to the orientation of signal-binding domains. Crystal packing analysis showed that TM-IclR dimers form a tetramer through interactions exclusively by signal-binding domains. A model is proposed for binding of IclR-like factors to DNA, and it suggests that signal-dependent transcription regulation is accomplished by affecting an oligomerization state of IclR and therefore its affinity for DNA target.

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Organizational Affiliation: 

Biosciences Division and Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IclR transcriptional regulator	A, B	249	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9WXS0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXS0  Go to UniProtKB:  Q9WXS0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	D [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.300 
• R-Value Work: 0.232 
• R-Value Observed: 0.257 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.229	α = 90
b = 61.076	β = 110.51
c = 95.911	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
SCALEPACK	data scaling
CNS	refinement
d*TREK	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-08-29 
• Released Date: 2002-09-11 
Deposition Author(s): Kim, Y., Zhang, R.G., Joachimiak, A., Skarina, T., Edwards, A., Savchenko, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 1JMR

Revision History  

• Version 1.0: 2002-09-11
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description