6P20 | pdb_00006p20

Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164

PDB DOI: https://doi.org/10.2210/pdb6P20/pdb

Classification: VIRAL PROTEIN
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.191 (Depositor), 0.193 (DCC)
R-Value Work:
0.148 (Depositor), 0.149 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Bacteriophage phiKZ gp163.1 PAAR repeat protein in complex with a T4 gp5 beta-helix fragment modified to mimic the phiKZ central spike gp164

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

To be published.

Macromolecule Content

Total Structure Weight: 44.61 kDa
Atom Count: 3,833
Modeled Residue Count: 415
Deposited Residue Count: 424
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baseplate central spike complex protein gp5,PHIKZ164	A, B, C	112	Tequatrovirus T4, Phikzvirus phiKZ This entity is chimeric	Mutation(s): 0 Gene Names: 5, PHIKZ164 EC: 3.2.1.17
UniProt
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009 Go to UniProtKB: P16009
Find proteins for Q8SCZ8 (Pseudomonas phage phiKZ) Explore Q8SCZ8 Go to UniProtKB: Q8SCZ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q8SCZ8 P16009
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PAAR-repeat central spike tip protein	D	88	Phikzvirus phiKZ	Mutation(s): 0
UniProt
Find proteins for L7T0L4 (Pseudomonas phage phiKZ) Explore L7T0L4 Go to UniProtKB: L7T0L4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L7T0L4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ELA Query on ELA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	Elaidic acid C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-MDZDMXLPSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B]	E [auth A], F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.191 (Depositor), 0.193 (DCC)
R-Value Work: 0.148 (Depositor), 0.149 (DCC)
R-Value Observed: 0.149 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.427	α = 90
b = 66.597	β = 90
c = 173.763	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Buth, S.A.

Shneider, M.M.

Leiman, P.G.

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

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2025-07-23
Changes: Derived calculations, Structure summary