9DRI | pdb_00009dri

Crystal structure of SphA in complex with VGQ intermedaite

• PDB DOI: https://doi.org/10.2210/pdb9DRI/pdb

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


• Deposited: 2024-09-25 Released: 2025-10-22 
• Deposition Author(s): Xi, W., Hai, Y.
• 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: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of SphA in complex with VGQ intermedaite

Xi, W., Hai, Y.

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

Macromolecule Content 

• Total Structure Weight: 108.05 kDa 
• Atom Count: 7,478 
• Modeled Residue Count: 920 
• Deposited Residue Count: 974 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
8-amino-7-oxononanoate synthase	A [auth B], B [auth C]	487	Aspergillus fumigatus	Mutation(s): 0  Gene Names: KXV57_002439 EC: 2.3.1.47
UniProt
Find proteins for A0A8H4HX52 (Aspergillus fumigatus) Explore A0A8H4HX52  Go to UniProtKB:  A0A8H4HX52

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BC7 (Subject of Investigation/LOI)	D [auth B], E [auth C]	(2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}but-3-enoic acid C12 H15 N2 O7 P LEPXTPTVSFKGPT-HMHNAJCMSA-N
TRS	C [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.2	α = 90
b = 71.873	β = 113.813
c = 90.531	γ = 90

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): Xi, W., Hai, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM151205

Revision History  

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