8F11: Endolysin

T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label. Determined by X-ray diffraction at 1.12 Å resolution. Released 15 Feb 2023.

Method: X-ray diffraction
Resolution: 1.12 Å
Organism: Escherichia phage T4
Chains: 1
Atoms: 1,813
Mol. weight: 19.14 kDa
Ligands: X8R
Released: 15 Feb 2023

Explore 8F11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F11 contains 10 α-helices and 6 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
β-strand	14-15	2	1
β-strand	16	1	2
β-strand	17-19	3	1
β-strand	25-28	4	1
β-strand	31-32	2	1
α-helix	39-50	12
β-strand	57	1	2
α-helix	60-80	21
α-helix	84-90	7
α-helix	93-106	14
α-helix	108-112	5
α-helix	115-122	8
α-helix	126-133	8
α-helix	137-141	5
α-helix	143-155	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Endolysin	A	protein	164	Escherichia phage T4	D9IEF7

Sequence of entity 1 (A), FASTA

>8F11_1 Endolysin (chains A)
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITK
DEAECLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRM
LQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL

Ligands and cofactors

ID	Name	Formula	Copies
X8R	1-[(1r,3r,5r,7r)-6-hydroxy-2,6-diazatricyclo[3.3.1.1~3,7~]decan-2-yl]ethan-1-one	C10 H16 N2 O2	1

Water and common crystallization additives (BME, K, CL) are not listed.

Primary citation

Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. Yang, Z., Stein, R.A., Pink, M. et al. J Am Chem Soc (2023) 145:25726-25736. DOI 10.1021/jacs.3c09184 · PubMed

Other PDB entries of the same protein (UniProt D9IEF7), best resolution first:

7LOG 0.99 Å, T4 lysozyme mutant L99A in complex with 3-butylpyridine
9DJK 1.04 Å, T4 Lysozyme D127H/V131H
7XE7 1.05 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH10
7LXA 1.07 Å, T4 lysozyme mutant L99A
9DJM 1.08 Å, T4 Lysozyme K147H/T151H
7XE6 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7
7XEA 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking
9DJI 1.1 Å, T4 Lysozyme R119H/Q123H
9DJD 1.11 Å, T4 Lysozyme A73H/G77H/Y139F co-crystallized with Cu(II)-NTA
9DJB 1.13 Å, T4 Lysozyme A73H/G77H
9DJC 1.13 Å, T4 Lysozyme A73H/G77H/Y139F
9DJP 1.17 Å, T4 Lysozyme A73H/G77H/R119H/Q123H co-crystallized with Cu(II)-NTA

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