2EQ9 | pdb_00002eq9

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdb

• PDB DOI: https://doi.org/10.2210/pdb2EQ9/pdb

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


• Deposited: 2007-03-30 Released: 2008-04-01 
• Deposition Author(s): Nakai, T., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of lipoamide dehydrogenase from Thermus thermophilus HB8

Nakai, T., Kamiya, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 417.3 kDa 
• Atom Count: 29,827 
• Modeled Residue Count: 3,840 
• Deposited Residue Count: 3,876 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase complex, dihydrolipoamide dehydrogenase E3 component	A, B, D, E, G, H, J, K	464	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0233 EC: 1.8.1.4
UniProt
Find proteins for Q5SLR0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLR0  Go to UniProtKB:  Q5SLR0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase complex, dihydrolipoamide acetyltransferase E2 component	C, F, I, L	41	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0232 EC: 2.3.1.168 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for Q5SLR1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLR1  Go to UniProtKB:  Q5SLR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	M [auth A], N [auth B], O [auth D], P [auth E], Q [auth G], R [auth H], S [auth J], T [auth K]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.781	α = 89.26
b = 88.877	β = 87.01
c = 144.149	γ = 70.84

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Nakai, T., Kamiya, N., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary