4YWN | pdb_00004ywn

Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

• PDB DOI: https://doi.org/10.2210/pdb4YWN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium avium 104
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-20 Released: 2015-04-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NADH-FMN oxidoreductase from Mycobacterium avium

Abendroth, J., Jensen, M., Arakaki, T.L., Lorimer, D.D., Edwards, T.E.

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: 35.04 kDa 
• Atom Count: 2,207 
• Modeled Residue Count: 279 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-fmn oxidoreductase	A, B	165	Mycobacterium avium 104	Mutation(s): 0  Gene Names: MAV_4912
UniProt
Find proteins for A0A0J9X290 (Mycobacterium avium (strain 104)) Explore A0A0J9X290  Go to UniProtKB:  A0A0J9X290

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.26	α = 90
b = 50.26	β = 90
c = 229.59	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2015-08-26
  Changes: Experimental preparation
• Version 1.2: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description