7E5Z | pdb_00007e5z

Dehydrogenase holoenzyme

• PDB DOI: https://doi.org/10.2210/pdb7E5Z/pdb
• EM Map EMD-30995: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Methylorubrum extorquens AM1
• Expression System: Methylorubrum extorquens AM1
• Mutation(s): No 


• Deposited: 2021-02-21 Released: 2022-02-23 
• Deposition Author(s): Roh, S.H., Park, J.S., Heo, Y.Y.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Dehydrogenase holoenzyme

Roh, S.H., Park, J.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 174.57 kDa 
• Atom Count: 10,244 
• Modeled Residue Count: 1,312 
• Deposited Residue Count: 1,567 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formate dehydrogenase	A	995	Methylorubrum extorquens AM1	Mutation(s): 0  Gene Names: fdh1A, MexAM1_META1p5032 EC: 1.17.1.9 (PDB Primary Data), 1.2.1.2 (UniProt)
UniProt
Find proteins for C5ATT7 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATT7  Go to UniProtKB:  C5ATT7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tungsten-containing formate dehydrogenase beta subunit	B	572	Methylorubrum extorquens AM1	Mutation(s): 0  Gene Names: fdh1B, MexAM1_META1p5031 EC: 1.2.1.2
UniProt
Find proteins for C5ATT6 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)) Explore C5ATT6  Go to UniProtKB:  C5ATT6

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGD	D [auth A], E [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C20 H26 N10 O13 P2 S2 VQAGYJCYOLHZDH-ILXWUORBSA-N
FMN	J [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SF4	G [auth A], H [auth A], I [auth A], K [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
W	C [auth A]	TUNGSTEN ION W FZFRVZDLZISPFJ-UHFFFAOYSA-N
FES	F [auth A], L [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15.0
MODEL REFINEMENT	PHENIX	1.19.1
MODEL REFINEMENT	Coot	0.8.9.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-23 
Deposition Author(s): Roh, S.H., Park, J.S., Heo, Y.Y.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2015M3D3A1A01064919

Revision History  

• Version 1.0: 2022-02-23
  Type: Initial release
  
• Version 1.1: 2022-03-02
  Changes: Database references, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary