3IC9 | pdb_00003ic9

The structure of dihydrolipoamide dehydrogenase from Colwellia psychrerythraea 34H.

• PDB DOI: https://doi.org/10.2210/pdb3IC9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Colwellia psychrerythraea 34H
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-17 Released: 2009-07-28 
• Deposition Author(s): Tan, K., Rakowski, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

The structure of dihydrolipoamide dehydrogenase from Colwellia psychrerythraea 34H.

Tan, K., Rakowski, E., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 220.92 kDa 
• Atom Count: 16,087 
• Modeled Residue Count: 1,926 
• Deposited Residue Count: 1,968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydrolipoamide dehydrogenase	A, B, C, D	492	Colwellia psychrerythraea 34H	Mutation(s): 0  Gene Names: Colwellia psychrerythraea, CPS_0826
UniProt
Find proteins for Q488E0 (Colwellia psychrerythraea (strain 34H / ATCC BAA-681)) Explore Q488E0  Go to UniProtKB:  Q488E0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], G [auth B], I [auth C], K [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NA	F [auth A], H [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.497	α = 90
b = 246.353	β = 90.2
c = 73.664	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Tan, K., Rakowski, E., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary