1YDN

Crystal Structure of the HMG-CoA Lyase from Brucella melitensis, Northeast Structural Genomics Target LR35.

Structural Biology Knowledgebase: 1YDN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.271

Literature

Macromolecules
Sequence Display for 1YDN

Classification: LYASE

Total Structure Weight: 126712.85

Macromolecule Entities
Molecule Chains Length Organism Details
HYDROXYMETHYLGLUTARYL-COA LYASE A, B, C, D 295 Brucella melitensis EC#: 4.1.3.4 IUBMB
Mutation: M10M, M64M, M82M, M189M, M256M, M260M
Gene Name(s): BMEI1926 BAWG_0314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A, B, C, D CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.271
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 82.27 α = 90.00
b = 86.40 β = 118.70
c = 87.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-24
  • Released Date: 2005-07-05
  • Deposition author(s): Forouhar, F., Abashidze, M., Hussain, M., Vorobiev, S.M., Xiao, R., Ciano, M., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name