2QHV | pdb_00002qhv

Structural Basis of Octanoic Acid Recognition by Lipoate-Protein Ligase B

• PDB DOI: https://doi.org/10.2210/pdb2QHV/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-07-03 Released: 2008-02-26 
• Deposition Author(s): Kim, D.J., Lee, S.J., Kim, H.S., Kim, K.H., Lee, H.H., Yoon, H.J., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structural basis of octanoic acid recognition by lipoate-protein ligase B

Kim, D.J., Lee, S.J., Kim, H.S., Kim, K.H., Lee, H.H., Yoon, H.J., Suh, S.W.

(2008) Proteins 70: 1620-1625

• PubMed: 18076036 
• DOI: https://doi.org/10.1002/prot.21843
• Primary Citation of Related Structures:  
  2QHS, 2QHT, 2QHU, 2QHV

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Organizational Affiliation: 
• Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.37 kDa 
• Atom Count: 1,858 
• Modeled Residue Count: 210 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoyltransferase	A	210	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTC 1746 EC: 2.3.1 (PDB Primary Data), 2.3.1.181 (UniProt)
UniProt
Find proteins for Q5SLQ3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ3  Go to UniProtKB:  Q5SLQ3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OC9	B [auth A]	OCTAN-1-OL C8 H18 O KBPLFHHGFOOTCA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.67	α = 90
b = 63.67	β = 90
c = 113.962	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-26 
Deposition Author(s): Kim, D.J., Lee, S.J., Kim, H.S., Kim, K.H., Lee, H.H., Yoon, H.J., Suh, S.W.

Revision History  

• Version 1.0: 2008-02-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations