1KGS

Crystal Structure at 1.50 A of an OmpR/PhoB Homolog from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb1KGS/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-11-28 Released: 2001-12-05 
• Deposition Author(s): Buckler, D.R., Zhou, Y., Stock, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.210 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

Evidence of intradomain and interdomain flexibility in an OmpR/PhoB homolog from Thermotoga maritima.

Buckler, D.R., Zhou, Y., Stock, A.M.

(2002) Structure 10: 153-164

• PubMed: 11839301 
• DOI: https://doi.org/10.1016/s0969-2126(01)00706-7
• Primary Citation of Related Structures:  
  1KGS


• PubMed Abstract: 
  

  Two-component systems, the predominant signal transduction strategy used by prokaryotes, involve phosphorelay from a sensor histidine kinase (HK) to an intracellular response regulator protein (RR) that typically acts as a transcription regulator. RRs are modular proteins, usually composed of a conserved regulatory domain, which functions as a phosphorylation-activated switch, and an attached DNA binding effector domain. The crystal structure of a Thermotoga maritima transcription factor, DrrD, has been determined at 1.5 A resolution, providing the first structural information for a full-length member of the OmpR/PhoB subfamily of RRs. A small interdomain interface occurs between alpha 5 of the regulatory domain and an antiparallel sheet of the effector domain. The lack of an extensive interface in the unphosphorylated protein distinguishes DrrD from other structurally characterized multidomain RRs and suggests a different mode of interdomain regulation.

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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.83 kDa 
• Atom Count: 2,016 
• Modelled Residue Count: 219 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA BINDING RESPONSE REGULATOR D	A	225	Thermotoga maritima	Mutation(s): 9  Gene Names: DRRD
UniProt
Find proteins for Q9WYN0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Go to UniProtKB:  Q9WYN0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.210 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.57	α = 90
b = 71.267	β = 106.56
c = 54.605	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-05 
Deposition Author(s): Buckler, D.R., Zhou, Y., Stock, A.M.

Revision History  

• Version 1.0: 2001-12-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary