3NR7 | pdb_00003nr7

Crystal structure of S. typhimurium H-NS 1-83

• PDB DOI: https://doi.org/10.2210/pdb3NR7/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-06-30 Released: 2010-09-01 
• Deposition Author(s): Arold, S.T., Leonard, P.G., Parkinson, G.N., Ladbury, J.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.304 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.271 (Depositor), 0.277 (DCC) 
• R-Value Observed: 
  0.274 (Depositor) 

Starting Model: experimental

Literature

H-NS forms a superhelical protein scaffold for DNA condensation.

Arold, S.T., Leonard, P.G., Parkinson, G.N., Ladbury, J.E.

(2010) Proc Natl Acad Sci U S A 107: 15728-15732

• PubMed: 20798056 
• DOI: https://doi.org/10.1073/pnas.1006966107
• Primary Citation Related Structures: 
  3NR7


• PubMed Abstract: 
  

  The histone-like nucleoid structuring (H-NS) protein plays a fundamental role in DNA condensation and is a key regulator of enterobacterial gene expression in response to changes in osmolarity, pH, and temperature. The protein is capable of high-order self-association via interactions of its oligomerization domain. Using crystallography, we have solved the structure of this complete domain in an oligomerized state. The observed superhelical structure establishes a mechanism for the self-association of H-NS via both an N-terminal antiparallel coiled-coil and a second, hitherto unidentified, helix-turn-helix dimerization interface at the C-terminal end of the oligomerization domain. The helical scaffold suggests the formation of a H-NS:plectonemic DNA nucleoprotein complex that is capable of explaining published biophysical and functional data, and establishes a unifying structural basis for coordinating the DNA packaging and transcription repression functions of H-NS.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Texas, M. D. Anderson Cancer Center, Houston, 77030, USA.

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 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 19.59 kDa 
• Atom Count: 1,288 
• Modeled Residue Count: 162 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein H-NS	A, B	86	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 1  Gene Names: H-NS, hns, hnsA, osmZ, STM1751
UniProt
Find proteins for P0A1S2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1S2  Go to UniProtKB:  P0A1S2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.304 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.271 (Depositor), 0.277 (DCC) 
• R-Value Observed: 0.274 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.397	α = 90
b = 130.397	β = 90
c = 55.061	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Arold, S.T., Leonard, P.G., Parkinson, G.N., Ladbury, J.E.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Refinement description