3R07 | pdb_00003r07

Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb3R07/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma acidophilum DSM 1728
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-07 Released: 2012-04-25 
• Deposition Author(s): Posner, M.G., Upadhyay, U., Crennell, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum

Posner, M.G., Upadhyay, A., Crennell, S., Danson, M.J., Bagby, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 43.61 kDa 
• Atom Count: 2,877 
• Modeled Residue Count: 343 
• Deposited Residue Count: 376 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoate-protein ligase A subunit 1	A	285	Thermoplasma acidophilum DSM 1728	Mutation(s): 0  Gene Names: lplA, Ta0514 EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for Q9HKT1 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKT1  Go to UniProtKB:  Q9HKT1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoate-protein ligase A subunit 2	B [auth C]	91	Thermoplasma acidophilum DSM 1728	Mutation(s): 0  Gene Names: Ta0513, Ta0513m EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt)
UniProt
Find proteins for Q9HKT2 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKT2  Go to UniProtKB:  Q9HKT2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	E [auth A], F [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.254 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.57	α = 90
b = 118.57	β = 90
c = 72.92	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Posner, M.G., Upadhyay, U., Crennell, S.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Structure summary
• Version 1.2: 2019-11-06
  Changes: Advisory, Data collection, Database references
• Version 1.3: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description