2CMP

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.276
R-Value Work: 0.225
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309113004399
Primary Citation of 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.

Organizational Affiliation

Laboratory of Bioorganic Chemistry and Crystallography, Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100 Bolzano, Italy. stefano.benini@unibz.it

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68928
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.276
R-Value Work: 0.225
R-Value Observed: 0.227
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Revision History (Full details and data files)

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