9Q0D | pdb_00009q0d

CryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution

• PDB DOI: https://doi.org/10.2210/pdb9Q0D/pdb
• EM Map EMD-72095: EMDB EMDataResource

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia cenocepacia
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-08-12 Released: 2025-09-17 
• Deposition Author(s): Abendroth, J., Davies, D.R., Yang, M., Hoarnyi, P.S., Lorimer, D.D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

CryoEM structure of methylmalonic acid semialdehyde dehydrogenase from Burkholderia cenocepacia at 2.38A resolution

Abendroth, J., Davies, D.R., Yang, M., Hoarnyi, P.S., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 223.14 kDa 
• Atom Count: 15,478 
• Modeled Residue Count: 1,988 
• Deposited Residue Count: 2,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methylmalonate-semialdehyde dehydrogenase (CoA acylating)	A, B, C, D	514	Burkholderia cenocepacia	Mutation(s): 0  Gene Names: msdA, BCAL1439 EC: 1.2.1.27
UniProt
Find proteins for B4E705 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E705  Go to UniProtKB:  B4E705

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0_5761
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Abendroth, J., Davies, D.R., Yang, M., Hoarnyi, P.S., Lorimer, D.D., Edwards, T.E., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release