4S0W | pdb_00004s0w

Wild type T4 lysozyme structure

PDB DOI: https://doi.org/10.2210/pdb4S0W/pdb

Classification: HYDROLASE
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-01-07 Released: 2015-02-04
Deposition Author(s): Snell, E.H., Snell, M.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.217 (Depositor), 0.219 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Wild type T4 lysozyme structure

Snell, E.H., Snell, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 38.57 kDa
Atom Count: 3,097
Modeled Residue Count: 324
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	A, B	164	Tequatrovirus T4	Mutation(s): 0 Gene Names: e, T4Tp126 EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00720
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], E [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	I [auth A], M [auth B], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	G [auth A], H [auth A], L [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.217 (Depositor), 0.219 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.63	α = 90
b = 52.63	β = 90
c = 99.46	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-02-04

Deposition Author(s):

Snell, E.H.

Snell, M.E.

Revision History (Full details and data files)

Version 1.0: 2015-02-04
Type: Initial release
Version 1.1: 2016-12-28
Changes: Database references, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description