9KF6 | pdb_00009kf6

Crystal structure of the reaction intermediate of Streptomyces sp. sulfotransferase Cpz4 involved in caprazamycins synthesis

• PDB DOI: https://doi.org/10.2210/pdb9KF6/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: 2.11 Å
• R-Value Free: 
  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the sulfate-covalent reaction intermediate of Streptomyces sp. sulfotransferase Cpz4 involved in Caprazamycins 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: 51.2 kDa 
• Atom Count: 3,702 
• Modeled Residue Count: 453 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfotransferase	A	472	Streptomyces sp.	Mutation(s): 0  Gene Names: cpz4
UniProt
Find proteins for D6N7U5 (Streptomyces sp. MK730-62F2) Explore D6N7U5  Go to UniProtKB:  D6N7U5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HS8	A	L-PEPTIDE LINKING	C6 H10 N3 O5 S		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.72	α = 90
b = 181.72	β = 90
c = 49.65	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