1NOX | pdb_00001nox

NADH OXIDASE FROM THERMUS THERMOPHILUS

• PDB DOI: https://doi.org/10.2210/pdb1NOX/pdb

• Classification: FLAVOENZYME
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-11-20 Released: 1997-03-12 
• Deposition Author(s): Hecht, H.J., Erdmann, H., Park, H.J., Sprinzl, M., Schmid, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.204 (Depositor) 
• R-Value Work: 
  0.182 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NADH oxidase from Thermus thermophilus.

Hecht, H.J., Erdmann, H., Park, H.J., Sprinzl, M., Schmid, R.D.

(1995) Nat Struct Biol 2: 1109-1114

• PubMed: 8846223 
• DOI: https://doi.org/10.1038/nsb1295-1109
• Primary Citation Related Structures: 
  1NOX


• PubMed Abstract: 
  

  The crystal structures of the flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) containing isoforms of NADH oxidase from Thermus thermophilus have been determined by isomorphous and molecular replacement and refined to 2.3 A and 1.6 A resolution with R-values of 18.5% and 18.6% respectively. The structure of the homodimeric enzyme consists of a central 4-stranded antiparallel beta-sheet covered by helices, a more flexible domain formed by two helices, and a C-terminal excursion connecting the subunits. The active sites are located in a deep cleft between the subunits. The binding site of the flavin cofactor lacks the common nucleotide binding fold and is different from the FMN binding site found in flavodoxins.

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Organizational Affiliation: 
• Department of Molecular Structure Research, GBF (Gesellschaft fr Biotechnologische, Forschung, Braunschweig, Germany.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 23.24 kDa 
• Atom Count: 1,695 
• Modeled Residue Count: 200 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH OXIDASE	A	205	Thermus thermophilus HB8	Mutation(s): 0  EC: 1.6.99.3 (PDB Primary Data), 7.1.1.2 (UniProt)
UniProt
Find proteins for Q60049 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q60049  Go to UniProtKB:  Q60049

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.204 (Depositor) 
• R-Value Work:  0.182 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.53	α = 90
b = 60.6	β = 90
c = 56.66	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
REFMAC	refinement
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
SCALA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-03-12 
Deposition Author(s): Hecht, H.J., Erdmann, H., Park, H.J., Sprinzl, M., Schmid, R.D.

Revision History  

• Version 1.0: 1997-03-12
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-04-03
  Changes: Refinement description