3W7X

Crystal structure of E. coli YgjK D324N complexed with melibiose

Structural Biology Knowledgebase: 3W7X SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 3W7X

Classification: HYDROLASE

Total Structure Weight: 172773.86

Macromolecule Entities
Molecule Chains Length Organism Details
Uncharacterized protein YgjK A, B 760 Escherichia coli EC#: 3.2.1 IUBMB
Mutation: D324N
Gene Name(s): ygjK b3080 JW3051
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 6-O-alpha-D-galactopyranosyl-alpha-D-glucopyranose
melibiose (Synonym)
C12 H22 O11
DLRVVLDZNNYCBX-CQHUIXDMSA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.249
  • R-Value Work: 0.189
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 62.14 α = 90.00
b = 138.16 β = 98.37
c = 86.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-08
  • Released Date: 2013-07-17
  • Deposition author(s): Miyazaki, T., Ichikawa, M., Yokoi, G., Kitaoka, M., Mori, H., Kitano, Y., Nishikawa, A., Tonozuka, T.

Revision History

  • 2014-03-12
    Type: Citation | Details: Citation update