2YQU | pdb_00002yqu

Crystal structures and evolutionary relationship of two different lipoamide dehydrogenase(E3s) from Thermus thermophilus

• PDB DOI: https://doi.org/10.2210/pdb2YQU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-03-31 Released: 2008-04-01 
• Deposition Author(s): Kondo, H., Hossain, M.T., Adachi, W., Nakai, T., Kamiya, N., Kuramitsu, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal structures and evolutionary relationship of two different lipoamide dehydrogenase(E3s) from Thermus thermophilus

Kondo, H., Hossain, M.T., Adachi, W., Nakai, T., Kamiya, N., Kuramitsu, S., Sekiguchi, T., Takenaka, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 100.1 kDa 
• Atom Count: 8,016 
• Modeled Residue Count: 910 
• Deposited Residue Count: 910 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoglutarate dehydrogenase E3 component	A, B	455	Thermus thermophilus HB8	Mutation(s): 0  EC: 1.8.1.4
UniProt
Find proteins for Q5SLK6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLK6  Go to UniProtKB:  Q5SLK6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PO4	G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CO3	C [auth A], E [auth B], F [auth B]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.411	α = 90
b = 105.76	β = 92.65
c = 84.907	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Kondo, H., Hossain, M.T., Adachi, W., Nakai, T., Kamiya, N., Kuramitsu, K.

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: 2024-10-23
  Changes: Structure summary