Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 44871.86 
• Atom Count: 3134 
• Residue Count: 408 
• Unique protein chains: 1

1JF9

Crystal Structure of selenocysteine lyase

• DOI: 10.2210/pdb1JF9/pdb

• Classification: LYASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2001-06-20 Released: 2001-07-04 
• Deposition Author(s): Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.207 
• R-Value Work: 0.178 

Literature

Analysis of the E. coli NifS CsdB Protein at 2.0A Reveals the Structural Basis for Perselenide and Persulfide Intermediate Formation

Lima, C.D.

(2002) J.Mol.Biol. 315: 1199-1208

• PubMed: 11827487 
• DOI: 10.1006/jmbi.2001.5308
• Primary Citation of Related Structures:  
  1KMK, 1KMJ


• PubMed Abstract: 
  

The Escherichia coli NifS CsdB protein is a member of the homodimeric pyridoxal 5'-phosphate (PLP)-dependent family of enzymes. These enzymes are capable of decomposing cysteine or selenocysteine into L-alanine and sulfur or selenium, respectively. E. coli NifS CsdB has a high specificity for L-selenocysteine in comparison to l-cysteine, suggesting a role for this enzyme is selenium metabolism. The 2.0 A crystal structure of E. coli NifS CsdB reveals a high-resolution view of the active site of this enzyme in apo-, persulfide, perselenide, and selenocysteine-bound intermediates, suggesting a mechanism for the stabilization of the enzyme persulfide and perselenide intermediates during catalysis, a necessary intermediate in the formation of sulfur and selenium containing metabolites.

---

Organizational Affiliation: 

Biochemistry Department and Structural Biology Program, Weill Medical College of Cornell University, New York, NY 10021, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SELENOCYSTEINE LYASE	A	408	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: sufS (csdB, ynhB) EC: 2.8.1.7
Find proteins for P77444 (Escherichia coli (strain K12)) Go to UniProtKB:  P77444

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PLP	A	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.207 
• R-Value Work: 0.178 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 126.375	α = 90.00
b = 126.375	β = 90.00
c = 133.578	γ = 90.00

Software Package:

Software Name	Purpose
SOLVE	phasing
SCALEPACK	data scaling
DENZO	data reduction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-06-20 
• Released Date: 2001-07-04 
• Deposition Author(s): Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History 

• Version 1.0: 2001-07-04
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance
• Version 1.3: 2015-01-21
  Type: Refinement description