5B52

Crystal structure of the N-terminal domain of H-NS family protein TurB

• PDB DOI: https://doi.org/10.2210/pdb5B52/pdb

• Classification: TRANSCRIPTION
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-21 Released: 2016-10-19 
• Deposition Author(s): Suzuki-Minakuchi, C., Nojiri, H.
• Funding Organization(s): Kato Memorial Bioscience Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.296 
• R-Value Work: 0.242 
• R-Value Observed: 0.245 

Literature

Structural similarities and differences in H-NS family proteins revealed by the N-terminal structure of TurB in Pseudomonas putida KT2440

Suzuki-Minakuchi, C., Kawazuma, K., Matsuzawa, J., Vasileva, D., Fujimoto, Z., Terada, T., Okada, K., Nojiri, H.

(2016) FEBS Lett 590: 3583-3594

• PubMed: 27709616 
• DOI: https://doi.org/10.1002/1873-3468.12425
• Primary Citation of Related Structures:  
  5B52


• PubMed Abstract: 
  

  H-NS family proteins play key roles in bacterial nucleoid compaction and global transcription. MvaT homologues in Pseudomonas have almost negligible amino acid sequence identity with H-NS, but can complement an hns-related phenotype of Escherichia coli. Here, we report the crystal structure of the N-terminal dimerization/oligomerization domain of TurB, an MvaT homologue in Pseudomonas putida KT2440. Our data identify two dimerization sites; the structure of the central dimerization site is almost the same as the corresponding region of H-NS, whereas the terminal dimerization sites are different. Our results reveal similarities and differences in dimerization and oligomerization mechanisms between H-NS and TurB.

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Organizational Affiliation: 

Biotechnology Research Center, The University of Tokyo, Japan. [e-mail].

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)

Macromolecule Content

• Total Structure Weight: 16.01 kDa 
• Atom Count: 955 
• Modelled Residue Count: 117 
• Deposited Residue Count: 138 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-NS family protein MvaT	A, B	69	Pseudomonas putida KT2440	Mutation(s): 1  Gene Names: PP_3765
UniProt
Find proteins for Q88GF9 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88GF9  Go to UniProtKB:  Q88GF9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.296 
• R-Value Work: 0.242 
• R-Value Observed: 0.245 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.555	α = 90
b = 143.35	β = 90
c = 75.637	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	model building
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data processing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Suzuki-Minakuchi, C., Nojiri, H.

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Funding Organization	Location	Grant Number
Kato Memorial Bioscience Foundation	Japan	--

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2016-11-09
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references