7W8J

Dimethylformamidase, 2x(A2B2)

• PDB DOI: https://doi.org/10.2210/pdb7W8J/pdb
• EM Map EMD-32357: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Paracoccus sp. SSG05
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-12-07 Released: 2022-04-06 
• Deposition Author(s): Vinothkumar, K.R., Subramanian, R., Arya, C., Ramanathan, G.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Dimethylformamidase with a Unique Iron Center

Arya, C., Ramanathan, G., Vinothkumar, K.R., Subramanian, R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 409.93 kDa 
• Atom Count: 28,678 
• Modelled Residue Count: 3,548 
• Deposited Residue Count: 3,628 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N,N-dimethylformamidase large subunit	A, C, E, G	775	Paracoccus sp. SSG05	Mutation(s): 0  Gene Names: dmfase2 EC: 3.5.1.56
UniProt
Find proteins for I6NT79 (Paracoccus sp. SSG05) Explore I6NT79  Go to UniProtKB:  I6NT79

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N,N-dimethylformamidase small subunit	B, D, F, H	132	Paracoccus sp. SSG05	Mutation(s): 0  Gene Names: dmfase1 EC: 3.5.1.56
UniProt
Find proteins for I6NWZ0 (Paracoccus sp. SSG05) Explore I6NWZ0  Go to UniProtKB:  I6NWZ0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	I [auth A], J [auth C], K [auth E], L [auth G]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	REFMAC	5.8.0267
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-06 
Deposition Author(s): Vinothkumar, K.R., Subramanian, R., Arya, C., Ramanathan, G.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	DBT/PR12422/MED/31/287/2014

Revision History  

• Version 1.0: 2022-04-06
  Type: Initial release
  
• Version 1.1: 2024-06-26
  Changes: Data collection, Refinement description