6DXP | pdb_00006dxp

The crystal structure of an FMN-dependent NADH-azoreductase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6DXP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-29 Released: 2018-07-25 
• Deposition Author(s): Arcinas, A.J., Ghosh, A., Chamala, S., Bonanno, J.B., Kelly, L., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of an FMN-dependent NADH-azoreductase from Klebsiella pneumoniae

Arcinas, A.J., Ghosh, A., Chamala, S., Bonanno, J.B., Kelly, L., Almo, S.C.

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)

Biological Assembly 2  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 98.86 kDa 
• Atom Count: 6,247 
• Modeled Residue Count: 815 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent NADH-azoreductase	A, B [auth C], C [auth B], D	223	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: azoR, B1727_12130, C3F39_21155 EC: 1.7 (PDB Primary Data), 1.6.5 (UniProt), 1.7.1.17 (UniProt)
UniProt
Find proteins for A6TCS9 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TCS9  Go to UniProtKB:  A6TCS9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.285 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.668	α = 90
b = 97.323	β = 90.71
c = 77.534	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-25 
Deposition Author(s): Arcinas, A.J., Ghosh, A., Chamala, S., Bonanno, J.B., Kelly, L., Almo, S.C.

Revision History  

• Version 1.0: 2018-07-25
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description