2IDB

Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.

Structural Biology Knowledgebase: 2IDB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 2IDB

Classification: LYASE

Total Structure Weight: 172942.08

Macromolecule Entities
Molecule Chains Length Organism Details
3-octaprenyl-4-hydroxybenzoate carboxy-lyase A, B, C 505 Escherichia coli EC#: 4.1.1.98 IUBMB
Mutation: M1M, M4M, M60M, M75M, M77M, M120M, M148M, M191M, M382M, M383M, M393M, M421M, M451M
Gene Name(s): ubiD yigC yigY b3843 JW3819
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, C 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-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 L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.201
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 194.29 α = 90.00
b = 194.29 β = 90.00
c = 106.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-09-14
  • Released Date: 2006-10-24
  • Deposition author(s): Zhou, W., Forouhar, F., Seetharaman, J, Fang, Y., Xiao, R., Cunningham, K., Ma, L.-C., Chen, C.X., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History

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