9IQ3 | pdb_00009iq3

AkaM,SnoaL-lile Protein

• PDB DOI: https://doi.org/10.2210/pdb9IQ3/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces sp. NPS-554
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-07-12 Released: 2025-07-16 
• Deposition Author(s): Zhang, B., Ma, X.X., Zhu, A., Ge, H.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.216 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: in silico

Literature

Structural and mechanistic insights into iminium-catalysed macrocyclization by nuclear transport factor 2-like enzymes

Liu, C.L., Zhang, B., Ge, H.M.

(2026) Nat Synth 

• DOI: https://doi.org/10.1038/s44160-025-00989-z

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.01 kDa 
• Atom Count: 3,632 
• Modeled Residue Count: 458 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AkaM	A, B, C, D	128	Streptomyces sp. NPS-554	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.216 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.167	α = 90
b = 74.167	β = 90
c = 108.275	γ = 90

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: 2025-07-16 
Deposition Author(s): Zhang, B., Ma, X.X., Zhu, A., Ge, H.M.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22277051,81925033, 22193071

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release
  
• Version 1.1: 2026-02-04
  Changes: Database references