9IXE

Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase without oxidized Cys86

• PDB DOI: https://doi.org/10.2210/pdb9IXE/pdb
• Entry: 9IXE supersedes: 9IQ9

• Classification: HYDROLASE
• Organism(s): Streptomyces lavendulae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-27 Released: 2024-11-20 
• Deposition Author(s): Oda, K., Matoba, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.216 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Copper inactivates DcsB by oxidizing the metal ligand Cys86 to sulfinic acid.

Oda, K., Matoba, Y.

(2024) FEBS J 

• DOI: https://doi.org/10.1111/febs.17325

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.36 kDa 
• Atom Count: 4,713 
• Modelled Residue Count: 546 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N(omega)-hydroxy-L-arginine amidinohydrolase	A, B	281	Streptomyces lavendulae	Mutation(s): 0  Gene Names: dcsB EC: 3.5.3.25
UniProt
Find proteins for D2Z025 (Streptomyces lavendulae) Explore D2Z025  Go to UniProtKB:  D2Z025

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU1 (Subject of Investigation/LOI)	F [auth B], G [auth B], H [auth B]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	C [auth A], D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.216 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.502	α = 83.57
b = 46.981	β = 84.69
c = 59.559	γ = 70.09

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Oda, K., Matoba, Y.
• This entry supersedes: 9IQ9

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release