Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 291.48 kDa 
• Atom Count: 19925 
• Modelled Residue Count: 2305 
• Deposited Residue Count: 2626 
• Unique protein chains: 3

1O94

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein

• DOI: 10.2210/pdb1O94/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Methylophilus methylotrophus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-11 Released: 2003-02-06 
• Deposition Author(s): Leys, D., Basran, J., Talfournier, F., Sutcliffe, M.J., Scrutton, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Extensive Conformational Sampling in a Ternary Electron Transfer Complex.

Leys, D., Basran, J., Talfournier, F., Sutcliffe, M.J., Scrutton, N.S.

(2003) Nat Struct Biol 10: 219

• PubMed: 12567183 
• DOI: 10.1038/nsb894
• Primary Citation of Related Structures:  
  1O94, 1O95, 1O96, 1O97


• PubMed Abstract: 
  

Here we report the crystal structures of a ternary electron transfer complex showing extensive motion at the protein interface. This physiological complex comprises the iron-sulfur flavoprotein trimethylamine dehydrogenase and electron transferring flavoprotein (ETF) from Methylophilus methylotrophus. In addition, we report the crystal structure of free ETF. In the complex, electron density for the FAD domain of ETF is absent, indicating high mobility. Positions for the FAD domain are revealed by molecular dynamics simulation, consistent with crystal structures and kinetic data. A dual interaction of ETF with trimethylamine dehydrogenase provides for dynamical motion at the protein interface: one site acts as an anchor, thereby allowing the other site to sample a large range of interactions, some compatible with rapid electron transfer. This study establishes the role of conformational sampling in multi-domain redox systems, providing insight into electron transfer between ETFs and structurally distinct redox partners.

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Organizational Affiliation: 

Department of Biochemistry, University of Leicester, University Road, Leicester LE1 7RH, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRIMETHYLAMINE DEHYDROGENASE	A, B	729	Methylophilus methylotrophus	Mutation(s): 0  Gene Names: tmd EC: 1.5.99.7 (PDB Primary Data), 1.5.8.2 (UniProt)
UniProt
Find proteins for P16099 (Methylophilus methylotrophus) Explore P16099  Go to UniProtKB:  P16099

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT	C, E	264	Methylophilus methylotrophus	Mutation(s): 0  Gene Names: etfB
UniProt
Find proteins for P53570 (Methylophilus methylotrophus) Explore P53570  Go to UniProtKB:  P53570

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT	D, F	320	Methylophilus methylotrophus	Mutation(s): 0  Gene Names: etfA
UniProt
Find proteins for P53571 (Methylophilus methylotrophus) Explore P53571  Go to UniProtKB:  P53571

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	G [auth A], J [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ADP (Subject of Investigation/LOI)	H [auth A], K [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SF4	I [auth A], L [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
AMP (Subject of Investigation/LOI)	M [auth C], N [auth E]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.212 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.93	α = 90
b = 211.543	β = 100.03
c = 125.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2002-12-11 
• Released Date: 2003-02-06 
Deposition Author(s): Leys, D., Basran, J., Talfournier, F., Sutcliffe, M.J., Scrutton, N.S.

Revision History  

• Version 1.0: 2003-02-06
  Type: Initial release
  
• Version 1.1: 2013-09-18
  Changes: Derived calculations, Non-polymer description, Other, Version format compliance