2C5R | pdb_00002c5r

The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA

• PDB DOI: https://doi.org/10.2210/pdb2C5R/pdb
• NAKB: 2C5R

• Classification: DNA-BINDING PROTEIN/DNA
• Organism(s): Salasvirus phi29
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-31 Released: 2005-11-08 
• Deposition Author(s): Albert, A., Jimenez, M., Munoz-Espin, D., Asensio, J.L., Hermoso, J.A., Salas, M., Meijer, W.J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.292 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Membrane Anchorage of Viral Phi 29 DNA During Replication.

Albert, A., Munoz-Espin, D., Jimenez, M., Asensio, J.L., Hermoso, J.A., Salas, M., Meijer, W.J.J.

(2005) J Biological Chem 280: 42486

• PubMed: 16275651 
• DOI: https://doi.org/10.1074/jbc.C500429200
• Primary Citation of Related Structures:  
  2C5R


• PubMed Abstract: 
  

  Prokaryotic DNA replication is compartmentalized at the cellular membrane. Functional and biochemical studies showed that the Bacillus subtilis phage 29-encoded membrane protein p16.7 is directly involved in the organization of membrane-associated viral DNA replication. The structure of the functional domain of p16.7 in complex with DNA, presented here, reveals the multimerization mode of the protein and provides insights in the organization of the phage genome at the membrane of the infected cell.

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Organizational Affiliation: 

Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 52.48 kDa 
• Atom Count: 3,535 
• Modelled Residue Count: 400 
• Deposited Residue Count: 418 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EARLY PROTEIN P16.7	A, B, C, D, E, F	67	Salasvirus phi29	Mutation(s): 0
UniProt
Find proteins for P16517 (Bacillus phage phi29) Explore P16517  Go to UniProtKB:  P16517

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*CP*AP*CP*CP*GP*GP)-3'	G [auth Y]	8	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*GP*TP*GP*GP*AP)-3'	H [auth Z]	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.292 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.505	α = 90
b = 72.111	β = 90
c = 127.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-08 
Deposition Author(s): Albert, A., Jimenez, M., Munoz-Espin, D., Asensio, J.L., Hermoso, J.A., Salas, M., Meijer, W.J.J.

Revision History  

• Version 1.0: 2005-11-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description