9LFI | pdb_00009lfi

Crystal structure of transaldolase AprG from Streptoalloteichus tenebrarius

• PDB DOI: https://doi.org/10.2210/pdb9LFI/pdb

• Classification: TRANSFERASE
• Organism(s): Streptoalloteichus tenebrarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-08 Released: 2025-09-24 
• Deposition Author(s): Xie, Z.Z., Li, Q.R., Zhang, L.L., Huang, J.-W., He, Y.T., Chen, C.-C., Guo, R.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: in silico

Literature

Apramycin Biosynthesis: Structure and Mechanism of Action of a New-Type Transaldolase AprG from Streptoalloteichus tenebrarius

Xie, Z., Zhang, L., Li, Q., Huang, J.W., He, Y., Zhang, H., Wang, X., Min, J., Chen, C.C., Guo, R.T.

(2025) ACS Catal : 16186-16196

• DOI: https://doi.org/10.1021/acscatal.5c02753

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 225.5 kDa 
• Atom Count: 16,407 
• Modeled Residue Count: 2,015 
• Deposited Residue Count: 2,070 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AprG	A, B, C, D, E, F	345	Streptoalloteichus tenebrarius	Mutation(s): 0  Gene Names: aprG
UniProt
Find proteins for Q6TDT8 (Streptoalloteichus tenebrarius (strain ATCC 17920 / DSM 40477 / JCM 4838 / CBS 697.72 / NBRC 16177 / NCIMB 11028 / NRRL B-12390 / A12253. 1 / ISP 5477)) Explore Q6TDT8  Go to UniProtKB:  Q6TDT8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG (Subject of Investigation/LOI)	G [auth A], H [auth C], I [auth C], J [auth D], K [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.784	α = 90
b = 142.005	β = 101.59
c = 129.821	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Xie, Z.Z., Li, Q.R., Zhang, L.L., Huang, J.-W., He, Y.T., Chen, C.-C., Guo, R.-T.

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

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release