PDB-6fhg: Crystal structure of the Ts2631 endolysin from Thermus scotoductu...

ID or keywords:

Entry

Database: PDB / ID: 6fhg

Title

Crystal structure of the Ts2631 endolysin from Thermus scotoductus phage with the unique N-terminal moiety responsible for peptidoglycan anchoring

Components

LysT endolysin

Keywords

ANTIMICROBIAL PROTEIN / Endolysin / thermophilic / N-terminal domain / T7-like fold

Function / homology

Function and homology information

N-acetylmuramoyl-L-alanine amidase / cytolysis in another organism / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / defense response to bacterium / zinc ion binding
Similarity search - Function

Biological species

Thermus phage 2631 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Zeth, K. / Sancho-Vaello, E. / Plotka, M.

Citation

Journal: Sci Rep / Year: 2019
Title: Structure and function of the Ts2631 endolysin of Thermus scotoductus phage vB_Tsc2631 with unique N-terminal extension used for peptidoglycan binding.
Authors: Plotka, M. / Sancho-Vaello, E. / Dorawa, S. / Kaczorowska, A.K. / Kozlowski, L.P. / Kaczorowski, T. / Zeth, K.

History

Deposition	Jan 14, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 30, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6fhg.cif.gz	144.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6fhg.ent.gz	115.1 KB	Display	PDB format
PDBx/mmJSON format	6fhg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6fhg_validation.pdf.gz	432.6 KB	Display	wwPDB validaton report
Full document	6fhg_full_validation.pdf.gz	434.7 KB	Display
Data in XML	6fhg_validation.xml.gz	14.4 KB	Display
Data in CIF	6fhg_validation.cif.gz	19.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fh/6fhg ftp://data.pdbj.org/pub/pdb/validation_reports/fh/6fhg	HTTPS FTP

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Related structure data

Related structure data	1lbaS S: Starting model for refinement
Similar structure data	5ftz-1 1aox-d 3fhk-5 5dui-d 3wv0-d 3td5-3 2bxj-d 3whd-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LysT endolysin

B: LysT endolysin

hetero molecules

36.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	53.579, 56.094, 116.715
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	LysT endolysin Mass: 18095.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage 2631 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A088FLK9
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.24 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350 and 0.2 mM di-sodium tartrate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.95→48.693 Å / Num. obs: 26266 / % possible obs: 91.7 % / Redundancy: 11.8 % / Net I/σ(I): 7.72
Reflection shell	Resolution: 1.95→2.02 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1LBA

1lba

Resolution: 1.95→48.693 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.15

	R_factor	Num. reflection	% reflection
R_free	0.2469	1246	5.13 %
R_work	0.2033	-	-
obs	0.2055	24301	92.12 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.95→48.693 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2527	0	2	122	2651

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2638
X-RAY DIFFRACTION	f_angle_d	1.057	3606
X-RAY DIFFRACTION	f_dihedral_angle_d	13.14	964
X-RAY DIFFRACTION	f_chiral_restr	0.044	368
X-RAY DIFFRACTION	f_plane_restr	0.006	463

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9498-2.0279	0.3725	146	0.3117	2719	X-RAY DIFFRACTION	100
2.0279-2.1202	0.3578	148	0.2907	2730	X-RAY DIFFRACTION	100
2.1202-2.232	0.3362	152	0.3056	2583	X-RAY DIFFRACTION	96
2.232-2.3718	0.34	45	0.2688	948	X-RAY DIFFRACTION	100
2.3718-2.5549	0.34	164	0.258	2755	X-RAY DIFFRACTION	100
2.5549-2.812	0.2925	149	0.248	2761	X-RAY DIFFRACTION	100
2.812-3.2188	0.2401	150	0.2251	2772	X-RAY DIFFRACTION	100
3.2188-4.0551	0.2118	142	0.1723	2830	X-RAY DIFFRACTION	100
4.0551-48.7086	0.1889	150	0.1515	2957	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.3775	-2.0604	-1.8962	8.7389	-1.3793	8.4511	0.2689	0.0668	0.5389	-0.8996	-0.2143	0.8644	-0.2227	-1.0824	0.0146	0.3541	0.013	-0.0719	0.3716	-0.0707	0.4388	32.1741	77.8552	49.4149
2	-0.143	0.7383	1.8314	0.7838	1.6563	3.6619	0.1401	-0.0665	0.319	0.2506	-0.0831	-0.5029	-0.7766	-0.57	-0.1286	0.5563	-0.03	-0.087	0.3172	0.03	0.5023	34.0104	57.4983	34.881
3	3.8003	-0.834	1.3999	1.536	-1.9575	9.4259	0.3133	0.2155	-0.2091	0.0387	-0.2089	-0.2236	0.2099	1.3524	-0.1335	0.3247	-0.0101	-0.0356	0.3332	0.0259	0.3292	43.5616	36.5469	35.5819
4	3.1867	0.7496	1.3051	4.1968	-0.5956	3.6942	-0.0958	-0.1446	0.2871	0.3774	0.0712	-0.4937	-0.4552	0.9126	0.1074	0.3364	-0.0895	-0.105	0.5169	-0.0343	0.4153	45.5767	46.5698	41.4452
5	2.3998	-0.6973	0.6983	5.9582	-2.0169	5.1623	0.0435	0.0274	0.1836	0.0187	-0.1963	-0.2169	-0.3135	0.6481	0.1125	0.266	-0.0446	-0.0264	0.2644	-0.0122	0.2712	37.9398	42.3924	34.3838
6	3.5443	-0.7777	0.0974	3.7081	0.7366	4.5754	0.1709	-0.1576	-0.884	-0.2695	-0.2607	-0.3205	1.1624	0.9387	0.1363	0.5065	0.1466	-0.008	0.3854	0.0246	0.4709	43.2405	25.6278	35.7043
7	4.0963	-1.445	1.7841	3.9213	-2.0613	3.9373	0.31	-0.0856	-0.52	-0.2644	-0.1518	0.6237	0.468	-0.0931	0.0057	0.3497	-0.0221	-0.0219	0.2218	-0.0651	0.3728	29.3168	32.0664	32.6005
8	7.2	-0.6334	-0.4672	3.2788	-0.2301	4.5323	0.1507	0.9595	0.0484	-0.6089	-0.2422	-0.0388	-0.1283	0.2585	0.0919	0.3929	0.0319	-0.0175	0.3997	-0.0215	0.2965	35.9565	39.5198	23.0796
9	5.3286	3.2338	-1.9083	4.0967	-5.0239	8.1869	-0.2073	-0.3609	-0.9931	-1.0582	-0.8257	-1.6172	0.9712	2.2302	0.9531	0.3642	0.0761	0.0557	0.8834	-0.0031	0.4409	46.9466	33.6995	26.3386
10	4.1518	2.8839	2.0582	3.4021	2.555	3.6558	-0.1643	0.6887	-0.653	-0.5297	0.4481	-0.2899	0.6997	0.744	-0.2978	0.4661	-0.0074	-0.0132	0.3654	-0.1118	0.3654	33.1272	25.4416	26.9518
11	2.5229	1.4856	1.0263	2.3539	-1.6894	7.7221	-0.1773	-1.0503	-0.0305	0.8306	-0.3428	0.6884	-0.1504	-0.7505	0.7366	0.4646	-0.0023	0.0192	0.3102	-0.0929	0.3834	31.7246	44.0088	44.9006
12	0.4056	-1.6178	-1.2831	3.76	3.0509	1.8769	0.2761	-0.1914	-0.2613	-0.2845	-0.1846	0.1624	0.3885	-0.5361	0.2411	0.4889	-0.0941	-0.0503	0.365	-0.0282	0.4459	33.131	62.3767	56.2659
13	1.2159	1.0154	-2.2169	0.756	-1.2667	5.2101	0.323	-0.6372	0.2486	0.1027	-0.4126	0.0591	-0.0437	0.8153	0.1301	0.3618	-0.1508	-0.0113	0.6682	0.031	0.3487	43.5234	81.9023	61.3601
14	8.5739	-3.3039	0.8424	2.6186	-1.1573	4.8387	0.2722	1.0115	0.0457	-0.2529	-0.8156	-0.9464	-0.1014	0.5339	0.5437	0.3486	0.0341	0.0227	0.4623	0.0595	0.3584	46.6096	75.8062	50.4867
15	4.1057	0.3685	-0.7009	3.3498	-0.5263	4.0968	0.1606	-0.514	0.0594	0.2623	-0.1598	-0.146	-0.1784	0.6022	0.0423	0.2257	-0.0269	-0.0183	0.3787	-0.0183	0.2978	40.2458	79.2913	56.0315
16	5.3741	0.8317	-0.2952	5.4933	-2.304	6.9185	0.3021	-0.6706	-0.5819	0.5168	-0.4006	-0.184	-0.1087	0.3728	0.1668	0.255	-0.0436	-0.0194	0.3605	-0.0075	0.3545	36.1795	70.6295	59.4835
17	4.7382	1.7624	-0.3778	4.7283	-1.0304	5.1537	0.3837	-0.9646	0.3412	0.4444	-0.3803	0.0173	-0.5569	0.28	0.0202	0.3448	-0.1327	0.0532	0.642	-0.1285	0.2961	36.6164	81.7898	66.7692
18	7.1492	-3.2005	-0.7163	4.7788	-2.4292	2.6584	0.3254	-1.2126	0.6906	0.9489	-0.9876	-1.1764	-0.5875	1.3739	0.4931	0.5135	-0.19	-0.0729	1.0832	0.0283	0.3957	46.6454	81.1326	70.8355
19	1.6891	-1.0553	1.3423	4.0823	-0.6646	1.0306	-0.3213	-2.0965	0.9676	1.0243	0.5517	0.6295	-0.3703	-0.4984	-0.1239	0.6948	-0.2568	0.1599	1.2355	-0.5566	0.5806	35.4816	90.3365	71.5246

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 10 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 25 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 39 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 40 through 59 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 60 through 93 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 94 through 106 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 107 through 122 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 134 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 135 through 144 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 145 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1 through 10 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 11 through 25 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 26 through 39 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 40 through 49 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 50 through 70 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 71 through 81 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 82 through 134 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 135 through 144 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 145 through 153 )

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