2Z33 | pdb_00002z33

Solution structure of the DNA complex of PhoB DNA-binding/transactivation Domain

• PDB DOI: https://doi.org/10.2210/pdb2Z33/pdb
• NAKB: 2Z33

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-31 Released: 2008-04-22 
• Deposition Author(s): Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations, structures with the lowest energy 

Literature

Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment.

Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A.

(2008) Proteins 71: 1970-1983

• PubMed: 18186481 
• DOI: https://doi.org/10.1002/prot.21874
• Primary Citation Related Structures: 
  2Z33


• PubMed Abstract: 
  

  The solution structure of the complex between the transcription factor PhoB DNA-binding/transactivation domain and DNA was determined by NMR spectroscopy and simulated annealing in a periodic boundary box of explicit water with the particle mesh Ewald method. The refined structures provided better convergence and better local geometry compared with the structures determined in vacuum. The hydrogen bond interactions between the PhoB domain and DNA in the aqueous environment were fully formed. The complex structure was found to be very similar to the crystal structure, particularly at the PhoB-DNA interface, much more so than expected from the vacuum structure. These results indicate the importance of the proper treatment of electrostatic and hydration influences in describing protein-DNA interactions. The hydration structures observed for the refined structures contained most of the crystal waters as a subset. We observed that various water-mediated PhoB-DNA interactions contributed to the molecular recognition between PhoB and DNA.

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Organizational Affiliation: 
• International Graduate School of Arts and Sciences, Yokohama City University, Yokohama, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.97 kDa 
• Atom Count: 1,504 
• Modeled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate regulon transcriptional regulatory protein phoB	C [auth A]	104	Escherichia coli	Mutation(s): 0  Gene Names: phoB
UniProt
Find proteins for P0AFJ5 (Escherichia coli (strain K12)) Explore P0AFJ5  Go to UniProtKB:  P0AFJ5

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*TP*GP*TP*CP*AP*TP*AP*AP*AP*TP*CP*TP*GP*T)-3'	A [auth B]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*AP*GP*AP*TP*TP*TP*AP*TP*GP*AP*CP*AP*GP*T)-3'	B [auth C]	16	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations, structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations
• Version 1.3: 2024-05-29
  Changes: Data collection