8J4V

Structure of Mycobacterium thermoresistibile NrdI(oxidised) determined at 1.1 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb8J4V/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Mycolicibacterium thermoresistibile
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-21 Released: 2024-10-09 
• Deposition Author(s): Yadav, L.R., Mande, S.C.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 0.158 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 

Starting Model: experimental

Literature

Structural insights into the initiation of free radical formation in the Class Ib ribonucleotide reductases in Mycobacteria

Yadav, L.R., Sharma, V., Shanmugam, M., Mande, S.C.

(2024) Curr Res Struct Biol 8: 100157

• DOI: https://doi.org/10.1016/j.crstbi.2024.100157

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: 17.09 kDa 
• Atom Count: 1,383 
• Modelled Residue Count: 145 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NrdI	A [auth C]	149	Mycolicibacterium thermoresistibile	Mutation(s): 0  Gene Names: nrdI
UniProt
Find proteins for G7CEK1 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)) Explore G7CEK1  Go to UniProtKB:  G7CEK1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN (Subject of Investigation/LOI)	B [auth C]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
PO4	C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	D [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 0.158 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.01	α = 90
b = 37.2	β = 111.61
c = 48.38	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Yadav, L.R., Mande, S.C.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	DST-NPDF (PDF/2015/000961) and DBT-Centre of Excellence Grant (BT/PR15450/COE/34/46/2016).

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release