4KU0 | pdb_00004ku0

Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with T4 gp5 beta-helix fragment

PDB DOI: https://doi.org/10.2210/pdb4KU0/pdb

Classification: HYDROLASE/PROTEIN BINDING
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-21 Released: 2014-05-21
Deposition Author(s): Buth, S.A., Leiman, P.G., Shneider, M.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.171 (Depositor), 0.164 (DCC)
R-Value Work:
0.132 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystall structute of the business end of the T4 cell-puncturing device

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

To be published.

Macromolecule Content

Total Structure Weight: 40.85 kDa
Atom Count: 3,531
Modeled Residue Count: 372
Deposited Residue Count: 384
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail-associated lysozyme	A, B, C	96	Tequatrovirus T4	Mutation(s): 0 Gene Names: 5 EC: 3.2.1.17
UniProt
Find proteins for P16009 (Enterobacteria phage T4) Explore P16009 Go to UniProtKB: P16009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16009
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region	D	96	Tequatrovirus T4	Mutation(s): 0 Gene Names: 5.4, y08B
UniProt
Find proteins for P39234 (Enterobacteria phage T4) Explore P39234 Go to UniProtKB: P39234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39234
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
ELA Query on ELA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	Elaidic acid C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-MDZDMXLPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	G [auth A], J [auth C], M [auth D], N [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.171 (Depositor), 0.164 (DCC)
R-Value Work: 0.132 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.302	α = 90
b = 49.327	β = 96.19
c = 84.057	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-21

Deposition Author(s):

Buth, S.A.

Leiman, P.G.

Shneider, M.M.

Revision History (Full details and data files)

Version 1.0: 2014-05-21
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2025-07-23
Changes: Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 4KU0 | pdb_00004ku0

Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with T4 gp5 beta-helix fragment

Crystall structute of the business end of the T4 cell-puncturing device

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2