9DQN | pdb_00009dqn

Nan Regulatory Protein (NanR) - DNA complex from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb9DQN/pdb
• NAKB: 9DQN

• Classification: TRANSCRIPTION/DNA
• Organism(s): Streptococcus pneumoniae, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-24 Released: 2025-08-20 
• 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: 2.99 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Nan Regulatory Protein (NanR) - DNA complex from Streptococcus pneumoniae (CASP target)

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: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS, assay for oligomerization, assay for oligomerization, assay for oligomerization

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 152.89 kDa 
• Atom Count: 10,176 
• Modeled Residue Count: 1,150 
• Deposited Residue Count: 1,204 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphosugar-binding transcriptional regulator	A, B [auth C], C [auth D], D [auth B]	283	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: ybbH, ybbH_1, SAMEA2467332_00633, SAMEA3176123_01518, SAMEA3176126_00944, SAMEA3176127_00886
UniProt
Find proteins for A0A0H2ZPE9 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore A0A0H2ZPE9  Go to UniProtKB:  A0A0H2ZPE9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')	E [auth H], G [auth J]	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')	F [auth I], H [auth K]	18	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	I [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	K [auth H], L [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.893	α = 90
b = 159.393	β = 90
c = 171.751	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
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: 2025-08-20
  Type: Initial release