2IDB | pdb_00002idb

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

• PDB DOI: https://doi.org/10.2210/pdb2IDB/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-14 Released: 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 172.94 kDa 
• Atom Count: 11,118 
• Modelled Residue Count: 1,385 
• Deposited Residue Count: 1,515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-octaprenyl-4-hydroxybenzoate carboxy-lyase	A, B, C	505	Escherichia coli K-12	Mutation(s): 13  Gene Names: ubiD, b3843 EC: 4.1.1 (PDB Primary Data), 4.1.1.98 (UniProt)
UniProt
Find proteins for P0AAB4 (Escherichia coli (strain K12)) Explore P0AAB4  Go to UniProtKB:  P0AAB4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	D [auth A], F [auth B], G [auth C]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
EDO	E [auth A], H [auth C], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.265 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.295	α = 90
b = 194.295	β = 90
c = 106.051	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• 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  

• Version 1.0: 2006-10-24
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary