9KF2 | pdb_00009kf2

Crystal structure of Streptomyces sp. sulfotransferase Cpz8 in complex with PAP, involved in Caprazamycin synthesis

• PDB DOI: https://doi.org/10.2210/pdb9KF2/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-05 Released: 2025-11-05 
• Deposition Author(s): Iwamoto, Y., Watanabe, M., Suzuki, K., Teramoto, T., Kakuta, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.142 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Streptomyces sp. sulfotransferase Cpz8 involved in Caprazamycin Synthesis

Iwamoto, Y., Watanabe, M., Kawano, K., Suzuki, K., Yazaki, M., Arisawa, M., Nishimoto, E., Igarashi, M., Teramoto, T., Kakuta, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.04 kDa 
• Atom Count: 2,167 
• Modeled Residue Count: 212 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfotransferase family protein	A	212	Streptomyces sp.	Mutation(s): 0  Gene Names: G3M58_47930
UniProt
Find proteins for A0A6G3X8Q2 (Streptomyces sp. SID7499) Explore A0A6G3X8Q2  Go to UniProtKB:  A0A6G3X8Q2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P (Subject of Investigation/LOI)	D [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
SO4 (Subject of Investigation/LOI)	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.142 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.983	α = 90
b = 44.161	β = 90
c = 101.272	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Iwamoto, Y., Watanabe, M., Suzuki, K., Teramoto, T., Kakuta, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	24K09353

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 2.0: 2025-11-12
  Changes: Atomic model