1K2X

Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene

Structural Biology Knowledgebase: 1K2X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.163

Literature

Macromolecules
Sequence Display for 1K2X

Classification: HYDROLASE

Total Structure Weight: 67139.18

Macromolecule Entities
Molecule Chains Length Organism Details
Putative L-asparaginase A, C 177 Escherichia coli EC#: 3.4.19.5 IUBMB
Fragment: N-TERMINUS (RESIDUES 2-178)
Mutation: C63X
Gene Name(s): iaaA spt ybiK b0828 JW0812
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Putative L-asparaginase B, D 143 Escherichia coli EC#: 3.4.19.5 IUBMB
Fragment: C-TERMINUS (RESIDUES 179-321)
Gene Name(s): iaaA spt ybiK b0828 JW0812

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

A, C, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, C SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A, C L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.198
  • R-Value Work: 0.163
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 50.30 α = 90.00
b = 77.62 β = 90.00
c = 148.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-30
  • Released Date: 2003-09-09
  • Deposition author(s): Borek, D., Jaskolski, M.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4