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)

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
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural study of sphA

Hai, Y., Xi, W., Chai, W., He, X.

To be published.

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

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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	3D Interactions
A1A8V (Subject of Investigation/LOI) Query on A1A8V Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	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		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]
GOL (Subject of Investigation/LOI) Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.