8TX9

Nan Regulatory Protein (core isomerase domain) from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb8TX9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2023-08-23 Released: 2024-09-11 
• Deposition Author(s): Wood, D.M., Horne, C.R., Panjikar, S., Dobson, R.C.J.
• Funding Organization(s): Royal Society of New Zealand, Ministry of Business, Innovation and Employment (New Zealand)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.271 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Structure of isomerase domain of the nan-regulatory protein (NanR) from Streptococcus pneumoniae

Wood, D.M., Dobson, R.C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 132.13 kDa 
• Atom Count: 6,252 
• Modelled Residue Count: 746 
• Deposited Residue Count: 1,135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MurR/RpiR family transcriptional regulator	A, B [auth C], C [auth D], D [auth B]	283	Streptococcus pneumoniae	Mutation(s): 0
UniProt
Find proteins for A0A064C3N8 (Streptococcus pneumoniae) Explore A0A064C3N8  Go to UniProtKB:  A0A064C3N8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMX (Subject of Investigation/LOI)	E [auth A], G [auth C], I [auth D], K [auth B]	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose C8 H16 N O9 P BRGMHAYQAZFZDJ-UOLFYFMNSA-N
NA	F [auth A], H [auth C], J [auth D], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B [auth C], C [auth D], D [auth B]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.271 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.577	α = 90
b = 147.577	β = 90
c = 82.311	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Wood, D.M., Horne, C.R., Panjikar, S., Dobson, R.C.J.

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Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	UOC1506
Ministry of Business, Innovation and Employment (New Zealand)	New Zealand	UOCX1706

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release