5DY2

Crystal structure of Dbr2 with mutation M27L

• PDB DOI: https://doi.org/10.2210/pdb5DY2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Artemisia annua
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-24 Released: 2016-10-05 
• Deposition Author(s): Li, L., Chen, T.T., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.190 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Starting Model: experimental

Literature

The Crystal structure of Dbr2

Li, L.

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: 43.09 kDa 
• Atom Count: 3,485 
• Modelled Residue Count: 378 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Artemisinic aldehyde Delta(11(13)) reductase	A	387	Artemisia annua	Mutation(s): 1  Gene Names: DBR2 EC: 1.3.1.92
UniProt
Find proteins for C5H429 (Artemisia annua) Explore C5H429  Go to UniProtKB:  C5H429

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
DIN	C [auth A]	1,6-DIHYDROXY NAPHTHALENE C10 H8 O2 FZZQNEVOYIYFPF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.190 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.62	α = 90
b = 81.02	β = 90
c = 86.53	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Li, L., Chen, T.T., Xu, Y.C.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description