9DOS | pdb_00009dos

Crystal structure of sphA with hydroVGQ

• PDB DOI: https://doi.org/10.2210/pdb9DOS/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Aspergillus fumigatus Af293
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-19 Released: 2025-10-22 
• Deposition Author(s): Hai, Y., Xi, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: in silico

Literature

Structural study of sphA

Hai, Y., Xi, W., Chai, W., He, X.

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)

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 215.96 kDa 
• Atom Count: 14,729 
• Modeled Residue Count: 1,852 
• Deposited Residue Count: 1,948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A, B, C, D	487	Aspergillus fumigatus Af293	Mutation(s): 0  Gene Names: AFUA_3G14690 EC: 2.3.1.47

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A8V (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth C], I [auth D]	(2Z)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]butanoic acid C12 H17 N2 O7 P MCYPVVOCEWZTOC-UVTDQMKNSA-N
GOL (Subject of Investigation/LOI)	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.903	α = 114.902
b = 91.375	β = 90.144
c = 90.157	γ = 93.424

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Hai, Y., Xi, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM151205

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release