6PGY

MTSL labelled T4 lysozyme pseudo-wild type K65C mutant

PDB DOI: https://doi.org/10.2210/pdb6PGY/pdb

Classification: HYDROLASE
Organism(s): Tequatrovirus T4
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2019-06-25 Released: 2020-07-01
Deposition Author(s): Cuneo, M.J., Myles, D.A., Li, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.182
R-Value Work: 0.158
R-Value Observed: 0.159

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

Making hydrogens stand out: Enhanced neutron diffraction from biological crystals using dynamic nuclear polarization

Pierce, J., Myles, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 19.09 kDa
Atom Count: 1,443
Modelled Residue Count: 162
Deposited Residue Count: 164
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin	A	164	Tequatrovirus T4	Mutation(s): 3 Gene Names: e, T4Tp126 EC: 3.2.1.17
UniProt
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7 Go to UniProtKB: D9IEF7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D9IEF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTN (Subject of Investigation/LOI) Query on MTN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate C₁₀ H₁₈ N O₃ S₂ MXZPGYFBZHBAQM-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
HED Query on HED 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]	2-HYDROXYETHYL DISULFIDE C₄ H₁₀ O₂ S₂ KYNFOMQIXZUKRK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.182
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.02	α = 90
b = 61.02	β = 90
c = 96.481	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Cuneo, M.J.

Myles, D.A.

Li, L.

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

6PGY

MTSL labelled T4 lysozyme pseudo-wild type K65C mutant

Making hydrogens stand out: Enhanced neutron diffraction from biological crystals using dynamic nuclear polarization

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)