2CMP | pdb_00002cmp

crystal structure of the DNA binding domain of G1P SMALL TERMINASE SUBUNIT from bacteriophage SF6

• PDB DOI: https://doi.org/10.2210/pdb2CMP/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Bacillus phage SF6
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2006-05-11 Released: 2007-05-15 
• Deposition Author(s): Benini, S., Chechik, M., Ortiz-Lombardia, M., Polier, S., Shevtsov, M.B., DeLuchi, D., Alonso, J.C., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.276 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

The 1.58 A Resolution Structure of the DNA-Binding Domain of Bacteriophage Sf6 Small Terminase Provides New Hints on DNA Binding

Benini, S., Chechik, M., Ortiz-Lombardia, M., Polier, S., Leech, A., Shevtsov, M.B., Alonso, J.C.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 376

• PubMed: 23545641 
• DOI: https://doi.org/10.1107/S1744309113004399
• Primary Citation Related Structures: 
  2CMP


• PubMed Abstract: 
  

  DNA packaging in tailed bacteriophages and in evolutionarily related herpesviruses is controlled by a viral-encoded terminase. As in a number of other phages, in the Bacillus subtilis bacteriophages SF6 and SPP1 the terminase complex consists of two proteins: G1P and G2P. The crystal structure of the N-terminal DNA-binding domain of the bacteriophage SF6 small terminase subunit G1P is reported. Structural comparison with other DNA-binding proteins allows a general model for the interaction of G1P with the packaging-initiation site to be proposed.

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Organizational Affiliation: 
• Laboratory of Bioorganic Chemistry and Crystallography, Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 6.96 kDa 
• Atom Count: 534 
• Modeled Residue Count: 56 
• Deposited Residue Count: 63 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TERMINASE SMALL SUBUNIT	A	63	Bacillus phage SF6	Mutation(s): 0
UniProt
Find proteins for P68928 (Bacillus phage SF6) Explore P68928  Go to UniProtKB:  P68928

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.276 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.286	α = 90
b = 57.286	β = 90
c = 57.286	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Benini, S., Chechik, M., Ortiz-Lombardia, M., Polier, S., Shevtsov, M.B., DeLuchi, D., Alonso, J.C., Antson, A.A.

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2013-04-10
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary
• Version 1.3: 2013-04-17
  Changes: Database references, Source and taxonomy
• Version 1.4: 2019-05-08
  Changes: Advisory, Data collection, Experimental preparation, Other
• Version 1.5: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.6: 2024-05-08
  Changes: Data collection, Database references, Other