5JDT: Endolysin

Structure of Spin-labelled T4 lysozyme mutant L118C-R1 at 100K. Determined by X-ray diffraction at 1.0 Å resolution. Released 28 Sept 2016.

Method: X-ray diffraction
Resolution: 1.0 Å
Organism: Enterobacteria phage T4
Chains: 1
Atoms: 1,983
Mol. weight: 19.19 kDa
Ligands: MTN, AZI
Released: 28 Sept 2016

Explore 5JDT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JDT contains 9 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: 9 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	85-90	6
α-helix	93-106	14
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	Enterobacteria phage T4	P00720

Sequence of entity 1 (A), FASTA

>5JDT_1 Endolysin (chains A)
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITK
DEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSCRM
LQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL

Ligands and cofactors

ID	Name	Formula	Copies
MTN	S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl]…	C10 H18 N O3 S2	1
AZI	Azide ion	N3	2

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

Primary citation

Tracking Transient Conformational States of T4 Lysozyme at Room Temperature Combining X-ray Crystallography and Site-Directed Spin Labeling. Consentius, P., Gohlke, U., Loll, B. et al. J Am Chem Soc (2016) 138:12868-12875. DOI 10.1021/jacs.6b05507 · PubMed

Other PDB entries of the same protein (UniProt P00720), best resolution first:

2O7A 0.84 Å, T4 lysozyme C-terminal fragment
7LOE 1.01 Å, T4 lysozyme mutant L99A in complex with 1-fluoranylnaphthalene
7LOD 1.02 Å, T4 lysozyme mutant L99A in complex with 1-fluoranyl-4-iodanyl-benzene
7LX8 1.03 Å, T4 lysozyme mutant L99A
5XPF 1.04 Å, High-resolution X-ray structure of the T26H mutant of T4 lysozyme
6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
7LOF 1.05 Å, T4 lysozyme mutant L99A in complex with 2-butylthiophene
7LX6 1.05 Å, T4 lysozyme mutant L99A
7LX7 1.05 Å, T4 lysozyme mutant L99A
1SWY 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Ab initio Structure…
1SWZ 1.06 Å, Use of an ion-binding site to bypass the 1000-atom limit to ab initio structure…
1SX2 1.06 Å, Use of a Halide Binding Site to Bypass the 1000-atom Limit to Structure Determination by…

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