3ZBQ | pdb_00003zbq

Protofilament of TubZ from Bacteriophage PhiKZ

• PDB DOI: https://doi.org/10.2210/pdb3ZBQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Phikzvirus phiKZ
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-12 Released: 2013-04-03 
• Deposition Author(s): Aylett, C.H.S., Lowe, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.203 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Structure of the Tubulin/Ftsz-Like Protein Tubz from Pseudomonas Bacteriophage Phikz

Aylett, C.H.S., Izore, T., Amos, L.A., Lowe, J.

(2013) J Mol Biology 425: 2164

• PubMed: 23528827 
• DOI: https://doi.org/10.1016/j.jmb.2013.03.019
• Primary Citation Related Structures: 
  3ZBP, 3ZBQ


• PubMed Abstract: 
  

  Pseudomonas ΦKZ-like bacteriophages encode a group of related tubulin/FtsZ-like proteins believed to be essential for the correct centring of replicated bacteriophage virions within the bacterial host. In this study, we present crystal structures of the tubulin/FtsZ-like protein TubZ from Pseudomonas bacteriophage ΦKZ in both the monomeric and protofilament states, revealing that ΦKZ TubZ undergoes structural changes required to polymerise, forming a canonical tubulin/FtsZ-like protofilament. Combining our structures with previous work, we propose a polymerisation-depolymerisation cycle for the Pseudomonas bacteriophage subgroup of tubulin/FtsZ-like proteins. Electron cryo-microscopy of ΦKZ TubZ filaments polymerised in vitro implies a long-pitch helical arrangement for the constituent protofilaments. Intriguingly, this feature is shared by the other known subgroup of bacteriophage tubulin/FtsZ-like proteins from Clostridium species, which are thought to be involved in partitioning the genomes of bacteriophages adopting a pseudo-lysogenic life cycle.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.74 kDa 
• Atom Count: 2,805 
• Modeled Residue Count: 315 
• Deposited Residue Count: 333 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHIKZ039	A	333	Phikzvirus phiKZ	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q8SDC3 (Pseudomonas phage phiKZ) Explore Q8SDC3  Go to UniProtKB:  Q8SDC3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.203 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.494	α = 90
b = 66.243	β = 112.69
c = 52.581	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Aylett, C.H.S., Lowe, J.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-04-10
  Changes: Database references
• Version 1.2: 2013-06-12
  Changes: Database references
• Version 2.0: 2018-01-24
  Changes: Atomic model, Source and taxonomy
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description