1KMK

E. coli NifS/CsdB protein at 2.20A with the cysteine perselenide intermediate (residue CSZ).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.196

Literature

Macromolecules
Sequence Display for 1KMK

Classification: LYASE

Total Structure Weight: 44974.75

Macromolecule Entities
Molecule Chains Length Organism Details
SELENOCYSTEINE LYASE A 406 Escherichia coli EC#: 2.8.1.7 IUBMB
Mutation: C364X
Gene Name(s): sufS csdB ynhB b1680 JW1670
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLP
Query on PLP

A PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SEC
Query on SEC

A SELENOCYSTEINE
C3 H7 N O2 Se
ZKZBPNGNEQAJSX-REOHCLBHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CSZ
Query on CSZ
A L-PEPTIDE LINKING C3 H7 N O2 S Se CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.196
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 125.86 α = 90.00
b = 125.86 β = 90.00
c = 133.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-16
  • Released Date: 2001-12-21
  • Deposition author(s): Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History

  • Version 1_0: 2001-12-21

    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: 2012-09-05

    Type: Database references

  • Version 1_4: 2014-04-09

    Type: Non-polymer description

  • Version 1_5: 2017-10-11

    Type: Refinement description