8R2J | pdb_00008r2j

X-ray crystallographic structure of SwaQ2 in complex with NADP+ and doxorubicin

• PDB DOI: https://doi.org/10.2210/pdb8R2J/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces swartbergensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-06 Released: 2024-08-07 
• Deposition Author(s): Schnell, R., Schneider, G.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.203 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation

Wandi, B.N., Dinis, P., Siitonen, V., Schneider, G., Schnell, R., Metsa-Ketele, M.

(2024) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.4c02623

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 66.54 kDa 
• Atom Count: 4,765 
• Modeled Residue Count: 549 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NmrA family transcriptional regulator	A, B	292	Streptomyces swartbergensis	Mutation(s): 0  Gene Names: CA983_01310
UniProt
Find proteins for A0A2C9ZNI9 (Streptomyces swartbergensis) Explore A0A2C9ZNI9  Go to UniProtKB:  A0A2C9ZNI9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	E [auth A], H [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
DM2 (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth B], G [auth B]	DOXORUBICIN C27 H29 N O11 AOJJSUZBOXZQNB-TZSSRYMLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.203 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.313	α = 90
b = 87.313	β = 90
c = 174.382	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Schnell, R., Schneider, G.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2018-03999

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release