9JHQ | pdb_00009jhq

Crystal structure of GodF, a post-translational modification enzyme involved in the biosynthesis of goadsporin

• PDB DOI: https://doi.org/10.2210/pdb9JHQ/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces sp. TP-A0584
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-10 Released: 2025-09-10 
• Deposition Author(s): Shimizu-Ibuka, A., Kato, Y.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: in silico

Literature

Structural analysis of GodF, a post-translational modification enzyme involved in the biosynthesis of goadsporin

Kato, Y., Shimizu-Ibuka, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 93.97 kDa 
• Atom Count: 6,393 
• Modeled Residue Count: 808 
• Deposited Residue Count: 867 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Goadsporin biosynthetic protein	A	867	Streptomyces sp. TP-A0584	Mutation(s): 0  Gene Names: godF
UniProt
Find proteins for Q3C2F5 (Streptomyces sp. TP-A0584) Explore Q3C2F5  Go to UniProtKB:  Q3C2F5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.34	α = 90
b = 69.67	β = 105.83
c = 75.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Shimizu-Ibuka, A., Kato, Y.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release