Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.54 kDa 
• Atom Count: 1063 
• Modelled Residue Count: 119 
• Deposited Residue Count: 131 
• Unique protein chains: 1

1DRM

CRYSTAL STRUCTURE OF THE LIGAND FREE BJFIXL HEME DOMAIN

• PDB DOI: 10.2210/pdb1DRM/pdb
• Entry: 1DRM supersedes: 1BV6

• Classification: TRANSFERASE
• Organism(s): Bradyrhizobium japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-06 Released: 2000-01-24 
• Deposition Author(s): Gong, W., Hao, B., Mansy, S.S., Gonzalez, G., Gilles-Gonzalez, M.A., Chan, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Structure of a biological oxygen sensor: a new mechanism for heme-driven signal transduction.

Gong, W., Hao, B., Mansy, S.S., Gonzalez, G., Gilles-Gonzalez, M.A., Chan, M.K.

(1998) Proc Natl Acad Sci U S A 95: 15177-15182

• PubMed: 9860942 
• DOI: 10.1073/pnas.95.26.15177
• Primary Citation of Related Structures:  
  1DRM


• PubMed Abstract: 
  

The FixL proteins are biological oxygen sensors that restrict the expression of specific genes to hypoxic conditions. FixL's oxygen-detecting domain is a heme binding region that controls the activity of an attached histidine kinase. The FixL switch is regulated by binding of oxygen and other strong-field ligands. In the absence of bound ligand, the heme domain permits kinase activity. In the presence of bound ligand, this domain turns off kinase activity. Comparison of the structures of two forms of the Bradyrhizobium japonicum FixL heme domain, one in the "on" state without bound ligand and one in the "off" state with bound cyanide, reveals a mechanism of regulation by a heme that is distinct from the classical hemoglobin models. The close structural resemblance of the FixL heme domain to the photoactive yellow protein confirms the existence of a PAS structural motif but reveals the presence of an alternative regulatory gateway.

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Organizational Affiliation: 

Department of Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENSOR PROTEIN FIXL	A	131	Bradyrhizobium japonicum	Mutation(s): 0  EC: 2.7.3 (PDB Primary Data), 2.7.13.3 (UniProt)
UniProt
Find proteins for P23222 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore P23222  Go to UniProtKB:  P23222

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.248 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.8	α = 90
b = 128.8	β = 90
c = 58.9	γ = 120

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-01-06 
• Released Date: 2000-01-24 
Deposition Author(s): Gong, W., Hao, B., Mansy, S.S., Gonzalez, G., Gilles-Gonzalez, M.A., Chan, M.K.
• This entry supersedes: 1BV6

Revision History  

• Version 1.0: 2000-01-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance