6P1Z | pdb_00006p1z

Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain

• PDB DOI: https://doi.org/10.2210/pdb6P1Z/pdb

• Classification: viral protein, hydrolase
• Organism(s): Tequatrovirus T4, Phikzvirus phiKZ
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-20 Released: 2020-05-27 
• Deposition Author(s): Buth, S.A., Shneider, M.M., Leiman, P.G.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with the C-terminal part of the T4 gp5 beta-helical domain

Buth, S.A., Shneider, M.M., Leiman, P.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.58 kDa 
• Atom Count: 6,324 
• Modelled Residue Count: 726 
• Deposited Residue Count: 752 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate central spike complex protein gp5	A, B, C, E, F, G	96	Tequatrovirus T4	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009  Go to UniProtKB:  P16009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PAAR-repeat central spike tip protein	D, H	88	Phikzvirus phiKZ	Mutation(s): 0
UniProt
Find proteins for L7T0L4 (Pseudomonas phage phiKZ) Explore L7T0L4  Go to UniProtKB:  L7T0L4

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STE	K [auth C], Q [auth G]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
ELA	L [auth C], O [auth E]	9-OCTADECENOIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-MDZDMXLPSA-N
PLM	J [auth B], P [auth E]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
ZN	M [auth D], R [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	I [auth A], N [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.275	α = 90
b = 69.123	β = 102.48
c = 77.802	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Buth, S.A., Shneider, M.M., Leiman, P.G.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_144243

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description