1ODD

OMPR C-TERMINAL DOMAIN (OMPR-C) FROM ESCHERICHIA COLI

• PDB DOI:  https://doi.org/10.2210/pdb1ODD/pdb

• Classification: GENE REGULATORY PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-10-31 Released: 1997-05-15 
• Deposition Author(s): Kondou, H., Nakagawa, A., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.296 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Escherichia coli positive regulator OmpR has a large loop structure at the putative RNA polymerase interaction site.

Kondo, H., Nakagawa, A., Nishihira, J., Nishimura, Y., Mizuno, T., Tanaka, I.

(1997) Nat Struct Biol 4: 28-31

• PubMed: 8989318 
• DOI: https://doi.org/10.1038/nsb0197-28
• Primary Citation of Related Structures:  
  1ODD


• PubMed Abstract: 
  

The C-terminal DNA-binding domain of OmpR, a positive regulator involved in osmoregulation expression of the ompF and ompC genes in Escherichia coli, has a helix-turn-helix variant motif. The 'turn' region, consisting of 11 residues, forms an RNA polymerase contact site.

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Related Citations: 

• Crystallization and X-Ray Studies of the DNA-Binding Domain of OmpR Protein, a Positive Regulator Involved in Activation of Osmoregulatory Genes in Escherichia Coli
  Kondo, H., Miyaji, T., Suzuki, M., Tate, S., Mizuno, T., Nishimura, Y., Tanaka, I.
  (1994) J Mol Biol 235: 780

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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.41 kDa 
• Atom Count: 862 
• Modelled Residue Count: 100 
• Deposited Residue Count: 118 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSCRIPTIONAL REGULATORY PROTEIN OMPR	A	118	Escherichia coli K-12	Mutation(s): 0  Gene Names: ompR, kmt, ompB, b3405, JW3368
UniProt
Find proteins for P0AA16 (Escherichia coli (strain K12)) Explore P0AA16  Go to UniProtKB:  P0AA16

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.296 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.16	α = 90
b = 59.16	β = 90
c = 58.4	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
SCALA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-05-15 
Deposition Author(s): Kondou, H., Nakagawa, A., Tanaka, I.

Revision History  

• Version 1.0: 1997-05-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance