8T0V | pdb_00008t0v

Closed state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

• PDB DOI: https://doi.org/10.2210/pdb8T0V/pdb
• EM Map EMD-40947: EMDB EMDataResource

• Classification: ISOMERASE
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-01 Released: 2024-07-03 
• Deposition Author(s): Tian, S., Tjia-Fleck, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Catalysis in Motion: Large-Scale Domain Shift Enables Co-C Bond Homolysis in Lysine 5,6-Aminomutase

Tian, S., Voss, P., Pham, K., Toba, D., Liu, M., Das, N., Yachuw, S., Denault, C., Klose, T., Uyeda, C., Tjia-Fleck, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 175.84 kDa 
• Atom Count: 10,985 
• Modeled Residue Count: 1,383 
• Deposited Residue Count: 1,558 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lysine 5,6-aminomutase alpha subunit	A, B	520	Caldanaerobacter subterraneus subsp. tengcongensis	Mutation(s): 0  Gene Names: TTE0726
UniProt
Find proteins for Q8RBT2 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBT2  Go to UniProtKB:  Q8RBT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-lysine 5,6-aminomutase beta subunit	C, D	259	Caldanaerobacter subterraneus subsp. tengcongensis	Mutation(s): 0  Gene Names: TTE0727
UniProt
Find proteins for Q8RBT3 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RBT3  Go to UniProtKB:  Q8RBT3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12 (Subject of Investigation/LOI)	G [auth D]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
X6I (Subject of Investigation/LOI)	F [auth B]	S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine C13 H20 N3 O7 P S BWEPWNLQXWSAOF-QZSDQICDSA-N
5AD (Subject of Investigation/LOI)	E [auth B]	5'-DEOXYADENOSINE C10 H13 N5 O3 XGYIMTFOTBMPFP-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Tian, S., Tjia-Fleck, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release
  
• Version 1.1: 2025-05-14
  Changes: Data collection, Structure summary
• Version 2.0: 2025-09-03
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Refinement description, Source and taxonomy, Structure summary