5E2F

Crystal Structure of Beta-lactamase class D from Bacillus subtilis

Structural Biology Knowledgebase: 5E2F SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.125

Literature

Macromolecules
Sequence Display for 5E2F

Classification: HYDROLASE

Total Structure Weight: 63057.09

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-lactamase YbxI A, B 270 Bacillus subtilis EC#: 3.5.2.6 IUBMB
Details: acylated lysine
Gene Name(s): ybxI ybdS BSU02090
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET
ALY
Query on ALY
A, B L-PEPTIDE LINKING C8 H16 N2 O3 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.125
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 47.70 α = 90.00
b = 68.86 β = 90.00
c = 153.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-10-01
  • Released Date: 2015-10-14
  • Deposition author(s): Kim, Y., Joachimiak, G., Endres, M., Babnigg, G., Joachimiak, A., MCSG, Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release