3PFT

Crystal Structure of Untagged C54A Mutant Flavin Reductase (DszD) in Complex with FMN From Mycobacterium goodii

• PDB DOI: https://doi.org/10.2210/pdb3PFT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium goodii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-10-29 Released: 2011-11-02 
• Deposition Author(s): Li, Q., Xu, P., Ma, C., Gu, L., Liu, X., Zhang, C., Li, N., Su, J., Li, B., Liu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

The flavin reductase DSZD from a desulfurizing mycobacterium goodii strain: systemic manipulation and investigation based on the crystal structure

Li, Q., Xu, P., Ma, C., Gu, L., Liu, X., Zhang, C., Li, N., Su, J., Li, B., Liu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 33.86 kDa 
• Atom Count: 2,880 
• Modelled Residue Count: 313 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavin reductase	A, B	157	Mycolicibacterium goodii	Mutation(s): 1  Gene Names: dszD EC: 1.5.1.29
UniProt
Find proteins for B6CDL6 (Mycolicibacterium goodii) Explore B6CDL6  Go to UniProtKB:  B6CDL6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.174	α = 90
b = 131.174	β = 90
c = 131.174	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
XFIT	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Li, Q., Xu, P., Ma, C., Gu, L., Liu, X., Zhang, C., Li, N., Su, J., Li, B., Liu, S.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations