9BUL

The structure of NiaR from Thermotoga maritima bound to nicotinic acid

• PDB DOI: https://doi.org/10.2210/pdb9BUL/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-17 Released: 2024-07-10 
• Deposition Author(s): Glasfeld, A., Cheng, D.W.C., Li, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.268 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

The structure of NiaR from Thermotoga maritima bound to nicotinic acid

Glasfeld, A., Cheng, D.W.C., Li, Y.

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.88 kDa 
• Atom Count: 1,347 
• Modelled Residue Count: 168 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcription repressor NiaR	A	175	Thermotoga maritima	Mutation(s): 0  Gene Names: niaR, TM_1602
UniProt
Find proteins for Q9X1T8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1T8  Go to UniProtKB:  Q9X1T8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIO (Subject of Investigation/LOI)	C [auth A]	NICOTINIC ACID C6 H5 N O2 PVNIIMVLHYAWGP-UHFFFAOYSA-N
PRO	D [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
FE2 (Subject of Investigation/LOI)	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.268 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.243	α = 90
b = 83.243	β = 90
c = 66.838	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Glasfeld, A., Cheng, D.W.C., Li, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release