PDB-8s3w: LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 ph...

ID or keywords:

Entry

Database: PDB / ID: 8s3w

Title

LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 phage vB_Tt72

Components

Lytic endopeptidase
gamma-D-Glu-m-A2pm-L-Lys-L-Arg

Keywords

VIRAL PROTEIN / Endopeptidase / Metalloprotein / Thermostability / Bacteriophage

Function / homology

PHOSPHATE ION

Function and homology information

Biological species

Thermus phage Tt72 (virus)

Escherichia coli BL21 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.394 Å

Authors

Rypniewski, W. / Biniek-Antosiak, K. / Bejger, M.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: LysTt72, a lytic endopeptidase from Thermus thermophilus MAT72 phage vB_Tt72
Authors: Rypniewski, W. / Biniek-Antosiak, K. / Bejger, M.

History

Deposition	Feb 20, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s3w.cif.gz	91 KB	Display	PDBx/mmCIF format
PDB format	pdb8s3w.ent.gz	64.4 KB	Display	PDB format
PDBx/mmJSON format	8s3w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s3w_validation.pdf.gz	451 KB	Display	wwPDB validaton report
Full document	8s3w_full_validation.pdf.gz	456.8 KB	Display
Data in XML	8s3w_validation.xml.gz	17.2 KB	Display
Data in CIF	8s3w_validation.cif.gz	22.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s3/8s3w ftp://data.pdbj.org/pub/pdb/validation_reports/s3/8s3w	HTTPS FTP

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Related structure data

Related structure data	8s3mC 8s3uC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/IPEQFH / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Lytic endopeptidase

C: gamma-D-Glu-m-A2pm-L-Lys-L-Arg

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.270, 60.870, 124.680
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lytic endopeptidase Mass: 39745.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus phage Tt72 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3)[pRARE] / References: EC: 3.4.24.32
#2: Protein/peptide	gamma-D-Glu-m-A2pm-L-Lys-L-Arg Mass: 605.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.08 Å³/Da / Density % sol: 40.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% v/v PEG 500 MME, 10% w/v PEG 20000, 30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfate, 0.1 M 6.5 imidazole/MES monohydrate (acid) at pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: cold nitrogen gas jet / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 28, 2023 / Details: focussing mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.39→99 Å / Num. obs: 13865 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC_1/2: 0.996 / R_rim(I) all: 0.194 / R_sym value: 0.186 / Net I/σ(I): 9.94
Reflection shell	Resolution: 2.39→2.49 Å / Mean I/σ(I) obs: 1.31 / Num. unique obs: 1947 / CC_1/2: 0.863 / R_rim(I) all: 1.849 / R_sym value: 1.774

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.394→62.34 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.923 / SU B: 14.86 / SU ML: 0.315 / Cross valid method: FREE R-VALUE / ESU R: 0.599 / ESU R Free: 0.32
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2811	664	4.789 %
R_work	0.1857	13201	-
all	0.19	-	-
obs	-	13865	99.791 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 63.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.747 Å²	0 Å²	0 Å²
2-	-	0.491 Å²	-0 Å²
3-	-	-	-5.238 Å²

Refinement step

Cycle: LAST / Resolution: 2.394→62.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2838	0	11	40	2889

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	2920
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2671
X-RAY DIFFRACTION	r_angle_refined_deg	1.689	1.813	3959
X-RAY DIFFRACTION	r_angle_other_deg	0.57	1.765	6152
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.167	5	344
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.346	5	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.459	10	472
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.833	10	142
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	421
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3437
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	729
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	691
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	2768
X-RAY DIFFRACTION	r_nbtor_refined	0.201	0.2	1441
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1578
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.264	0.2	121
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.122	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.237	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.218	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.224	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	5.668	6.177	1382
X-RAY DIFFRACTION	r_mcbond_other	5.652	6.177	1382
X-RAY DIFFRACTION	r_mcangle_it	8.235	11.085	1724
X-RAY DIFFRACTION	r_mcangle_other	8.236	11.086	1725
X-RAY DIFFRACTION	r_scbond_it	6.297	6.731	1538
X-RAY DIFFRACTION	r_scbond_other	6.289	6.719	1535
X-RAY DIFFRACTION	r_scangle_it	9.322	12.135	2235
X-RAY DIFFRACTION	r_scangle_other	9.32	12.139	2236
X-RAY DIFFRACTION	r_lrange_it	12.061	62.215	3404
X-RAY DIFFRACTION	r_lrange_other	12.059	62.228	3405

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.394-2.456	0.477	57	0.393	967	0.398	1031	0.798	0.844	99.3211	0.383
2.456-2.523	0.404	38	0.355	923	0.357	961	0.837	0.887	100	0.347
2.523-2.596	0.477	46	0.313	916	0.321	962	0.825	0.911	100	0.298
2.596-2.676	0.313	44	0.285	875	0.286	919	0.901	0.929	100	0.269
2.676-2.764	0.362	39	0.258	873	0.262	913	0.903	0.941	99.8905	0.239
2.764-2.861	0.324	37	0.218	812	0.223	850	0.923	0.959	99.8824	0.197
2.861-2.968	0.342	35	0.194	810	0.2	845	0.946	0.971	100	0.174
2.968-3.089	0.341	34	0.176	774	0.182	809	0.914	0.977	99.8764	0.156
3.089-3.226	0.345	41	0.174	753	0.181	794	0.92	0.977	100	0.151
3.226-3.383	0.311	38	0.181	714	0.187	752	0.941	0.977	100	0.161
3.383-3.566	0.277	31	0.166	679	0.171	710	0.957	0.983	100	0.154
3.566-3.781	0.263	41	0.175	633	0.18	674	0.956	0.982	100	0.162
3.781-4.041	0.209	29	0.143	619	0.146	650	0.964	0.987	99.6923	0.134
4.041-4.364	0.19	29	0.132	567	0.134	596	0.976	0.989	100	0.129
4.364-4.778	0.215	38	0.147	499	0.152	553	0.973	0.985	97.1067	0.147
4.778-5.338	0.348	24	0.163	489	0.17	513	0.948	0.983	100	0.172
5.338-6.156	0.365	20	0.191	433	0.197	453	0.947	0.98	100	0.195
6.156-7.521	0.239	21	0.164	377	0.168	398	0.953	0.981	100	0.177
7.521-10.56	0.18	13	0.151	299	0.153	312	0.987	0.985	100	0.178
10.56-62.34	0.319	9	0.239	190	0.243	199	0.953	0.959	100	0.321

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