6P20

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baseplate central spike complex protein gp5,PHIKZ164
A, B, C
112Tequatrovirus T4Phikzvirus phiKZ
This entity is chimeric
Mutation(s): 0 
Gene Names: 5PHIKZ164
EC: 3.2.1.17
UniProt
Find proteins for Q8SCZ8 (Pseudomonas phage phiKZ)
Explore Q8SCZ8 
Go to UniProtKB:  Q8SCZ8
Find proteins for P16009 (Enterobacteria phage T4)
Explore P16009 
Go to UniProtKB:  P16009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ8SCZ8P16009
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PAAR-repeat central spike tip protein88Phikzvirus phiKZMutation(s): 0 
UniProt
Find proteins for L7T0L4 (Pseudomonas phage phiKZ)
Explore L7T0L4 
Go to UniProtKB:  L7T0L4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7T0L4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download Ideal Coordinates CCD File 
G [auth A]STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
ELA
Query on ELA

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H [auth A]9-OCTADECENOIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-MDZDMXLPSA-N
PLM
Query on PLM

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K [auth B]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
ZN
Query on ZN

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L [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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I [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.427α = 90
b = 66.597β = 90
c = 173.763γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_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