9IVH | pdb_00009ivh

Structure of TF9 mutant of aminotransferase from Mycolicibacterium neoaurum in complex with LLP and G4O

• PDB DOI: https://doi.org/10.2210/pdb9IVH/pdb

• Classification: TRANSFERASE
• Organism(s): Mycolicibacterium neoaurum VKM Ac-1815D
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-07-23 Released: 2025-07-30 
• Deposition Author(s): Wei, H., Cong, L., You, S., Liu, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: in silico

Literature

Structure of TF9 mutant of aminotransferase from Mycolicibacterium neoaurum in complex with LLP and G4O

Wei, H., Cong, L., You, S., Liu, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 142.8 kDa 
• Atom Count: 10,650 
• Modeled Residue Count: 1,245 
• Deposited Residue Count: 1,292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain amino acid transferase	A, B, C, D	323	Mycolicibacterium neoaurum VKM Ac-1815D	Mutation(s): 0  Gene Names: D174_04695
UniProt
Find proteins for V5X927 (Mycolicibacterium neoaurum VKM Ac-1815D) Explore V5X927  Go to UniProtKB:  V5X927

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4O (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	propan-2-amine C3 H9 N JJWLVOIRVHMVIS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.615	α = 96.96
b = 78.586	β = 108.42
c = 91.541	γ = 113.07

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Wei, H., Cong, L., You, S., Liu, W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release