9IQL | pdb_00009iql

SacM in complex with L6S

• PDB DOI: https://doi.org/10.2210/pdb9IQL/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Saccharothrix syringae
• 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., Ge, H.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Tandem Michael addition and Knoevenagel condensation catalyzed by NTF2-Like Enzymes as iminium catalysis

Liu, C.L., Zhang, B., Ge, H.M.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 30.93 kDa 
• Atom Count: 2,162 
• Modeled Residue Count: 246 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear transport factor 2 family protein	A, B	133	Saccharothrix syringae	Mutation(s): 0  Gene Names: EKG83_24495
UniProt
Find proteins for A0A5Q0H2K6 (Saccharothrix syringae) Explore A0A5Q0H2K6  Go to UniProtKB:  A0A5Q0H2K6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D90 (Subject of Investigation/LOI)	C [auth A], F [auth B]	(5~{R},6~{R})-6-[(~{E})-5-[(2~{S},3~{S},5~{S})-5-(2-hydroxyethyl)-3,5-dimethyl-oxolan-2-yl]-3-methyl-2-oxidanylidene-pent-3-enyl]-5-propyl-oxane-2,4-dione C22 H34 O6 MVJVJKSGEMISOL-KHRHQXNTSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.239	α = 90
b = 52.239	β = 90
c = 203.458	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Zhang, B., Ge, H.M.

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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: 2025-10-15
  Changes: Structure summary