2Z3X | pdb_00002z3x

Structure of a Protein-DNA Complex Essential for DNA Protection in Spore of Bacillus Species

• PDB DOI: https://doi.org/10.2210/pdb2Z3X/pdb
• NAKB: 2Z3X

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): synthetic construct, Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-06-08 Released: 2008-02-12 
• Deposition Author(s): Lee, K.S., Jedrzejas, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.283 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Structure of a protein-DNA complex essential for DNA protection in spores of Bacillus species.

Lee, K.S., Bumbaca, D., Kosman, J., Setlow, P., Jedrzejas, M.J.

(2008) Proc Natl Acad Sci U S A 105: 2806-2811

• PubMed: 18287075 
• DOI: https://doi.org/10.1073/pnas.0708244105
• Primary Citation Related Structures: 
  2Z3X


• PubMed Abstract: 
  

  The DNA-binding alpha/beta-type small acid-soluble proteins (SASPs) are a major factor in the resistance and long-term survival of spores of Bacillus species by protecting spore DNA against damage due to desiccation, heat, toxic chemicals, enzymes, and UV radiation. We now report the crystal structure at 2.1 A resolution of an alpha/beta-type SASP bound to a 10-bp DNA duplex. In the complex, the alpha/beta-type SASP adopt a helix-turn-helix motif, interact with DNA through minor groove contacts, bind to approximately 6 bp of DNA as a dimer, and the DNA is in an A-B type conformation. The structure of the complex provides important insights into the molecular details of both DNA and alpha/beta-type SASP protection in the complex and thus also in spores.

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Organizational Affiliation: 
• Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.74 kDa 
• Atom Count: 1,698 
• Modeled Residue Count: 190 
• Deposited Residue Count: 211 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Small, acid-soluble spore protein C	C [auth A], D [auth B], E [auth C]	63	Bacillus subtilis	Mutation(s): 2  Gene Names: sspC
UniProt
Find proteins for P02958 (Bacillus subtilis (strain 168)) Explore P02958  Go to UniProtKB:  P02958

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*A)-3'	A [auth D]	11	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*A)-3'	B [auth E]	11	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.283 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.962	α = 90
b = 86.962	β = 90
c = 144.669	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Lee, K.S., Jedrzejas, M.J.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-10-24
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.3: 2021-11-10
  Changes: Database references
• Version 1.4: 2024-05-29
  Changes: Data collection