4AIV

Crystal Structure of putative NADH-dependent nitrite reductase small subunit from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4AIV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-15 Released: 2012-09-12 
• Deposition Author(s): Izumi, A., Schnell, R., Schneider, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.245 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Crystal Structure of Nird, the Small Subunit of the Nitrite Reductase Nirbd from Mycobacterium Tuberculosis, at 2.0 Angstrom Resolution

Izumi, A., Schnell, R., Schneider, G.

(2012) Proteins 80: 2799

• PubMed: 22965870 
• DOI: https://doi.org/10.1002/prot.24177
• Primary Citation of Related Structures:  
  4AIV


• PubMed Abstract: 
  

  NirD is part of the nitrite reductase complex NirBD that catalyses the reduction of nitrite to NH(3) in nitrate assimilation and anaerobic respiration. The crystal structure analysis of NirD from Mycobacterium tuberculosis shows a double β-sandwich fold. NirD is related in three-dimensional structure and sequence to the Rieske proteins; however, it does not contain any Fe-S cluster or other cofactors that might be involved in electron transfer. A cysteine residue at the protein surface, conserved in NirD homologues lacking the iron-sulfur cluster might be important for the interaction with NirB and possibly stabilize one of the Fe-S centers in this subunit.

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Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.

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: 12.59 kDa 
• Atom Count: 920 
• Modelled Residue Count: 113 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROBABLE NITRITE REDUCTASE [NAD(P)H] SMALL SUBUNIT NIRD	A	119	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  EC: 1.6.6.4
UniProt
Find proteins for O53675 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53675  Go to UniProtKB:  O53675

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.245 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.104	α = 90
b = 35.104	β = 90
c = 180.392	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-12 
Deposition Author(s): Izumi, A., Schnell, R., Schneider, G.

Revision History  

• Version 1.0: 2012-09-12
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 1.2: 2012-11-14
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description