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: 15.62 kDa 
• Atom Count: 1006 
• Modelled Residue Count: 116 
• Deposited Residue Count: 131 
• Unique protein chains: 1

1LSX

Crystal structure of the methylimidazole-bound BjFixL heme domain

• PDB DOI: 10.2210/pdb1LSX/pdb

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


• Deposited: 2002-05-20 Released: 2002-11-20 
• Deposition Author(s): Hao, B., Isaza, C., Arndt, J., Soltis, M., Chan, M.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 

Literature

Structure-based mechanism of O2 sensing and ligand discrimination by the FixL heme domain of Bradyrhizobium japonicum

Hao, B., Isaza, C., Arndt, J., Soltis, M., Chan, M.K.

(2002) Biochemistry 41: 12952-12958

• PubMed: 12390021 
• DOI: 10.1021/bi020144l
• Primary Citation of Related Structures:  
  1LSV, 1LSW, 1LSX, 1LT0


• PubMed Abstract: 
  

Structures of the Bradyrhizobium japonicum FixL heme domain have been determined in the absence and presence of specific ligands to elucidate the detailed features of its O2 sensing mechanism. The putative roles of spin-state and steric hindrance were evaluated by the structure determination of ferrous CO-bound BjFixLH and correlating its features with other ligand-bound structures. As found for NO-BjFixLH, no protein conformational change was observed in CO-BjFixLH, suggesting a more complicated mechanism than solely spin state or ligand sterics. To evaluate the role of oxidation state, the structure of the ferrous deoxy-BjFixLH was determined. The structure of deoxy-BjFixLH was found to be virtually identical to the structure of the ferric met-BjFixLH. The role of hydrogen bonding of substrates to a heme-pocket water was evaluated by determining the structure of BjFixLH bound to 1-methyl-imidazole that cannot form a hydrogen bond with this water. In this case, the heme-mediated conformational change was observed, limiting the potential importance of this interaction. Finally, the structure of cyanomet-BjFixLH was revisited to rule out concerns regarding the partial occupancy of the cyanide ligand in a previous structure. In the revised structure, Arg 220 was found to move into the heme pocket to form a hydrogen bond to the bound cyanide ligand. The implications of these results on FixL's sensing mechanism are discussed.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensor protein FixL	A	131	Bradyrhizobium japonicum	Mutation(s): 0  Gene Names: fixL 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 2 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
1MZ	C [auth A]	1-METHYLIMIDAZOLE C4 H7 N2 MCTWTZJPVLRJOU-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.02	α = 90
b = 127.02	β = 90
c = 58.62	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-05-20 
• Released Date: 2002-11-20 
Deposition Author(s): Hao, B., Isaza, C., Arndt, J., Soltis, M., Chan, M.K.

Revision History  

• Version 1.0: 2002-11-20
  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: 2017-02-01
  Changes: Structure summary