8V4V | pdb_00008v4v

Nan Regulatory Protein Full-length from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb8V4V/pdb

• Classification: TRANSCRIPTION
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-29 Released: 2024-12-04 
• Deposition Author(s): Wood, D.M., Dobson, R.C.J., Horne, C.R.
• 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: 2.95 Å
• R-Value Free: 
  0.301 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Structure of full-length nan-regulatory protein (NanR) from Streptococcus pneumoniae

Wood, D.M., Dobson, R.C.J., Horne, C.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 65.99 kDa 
• Atom Count: 3,753 
• Modeled Residue Count: 462 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphosugar-binding transcriptional regulator	A [auth B], B [auth A]	283	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ybbH_2
UniProt
Find proteins for A0A0H2ZPE9 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZPE9  Go to UniProtKB:  A0A0H2ZPE9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BMX (Subject of Investigation/LOI)	C [auth B], F [auth A]	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose C8 H16 N O9 P BRGMHAYQAZFZDJ-UOLFYFMNSA-N
CL	D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth B], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.301 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.873	α = 90
b = 223.646	β = 90
c = 52.734	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Wood, D.M., Dobson, R.C.J., Horne, C.R.

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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: 2024-12-04
  Type: Initial release