2IDB

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

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)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-octaprenyl-4-hydroxybenzoate carboxy-lyase
A, B, C
505Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ubiD (yigC, yigY)
EC: 4.1.1.98
Find proteins for P0AAB4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AAB4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A, B, C
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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
Unit Cell:
Length (Å)Angle (°)
a = 194.295α = 90.00
b = 194.295β = 90.00
c = 106.051γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
SOLVEphasing
SnBphasing
HKL-2000data reduction
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Database references, Refinement description, Structure summary