PDB-8vsq: Crystal structure of Esub1

ID or keywords:

Entry

Database: PDB / ID: 8vsq

Title

Crystal structure of Esub1

Components

Esub1

Keywords

UNKNOWN FUNCTION / Streptococcus pyogenes / dimer / DNA binding domain

Function / homology

Type I restriction-modification system, specificity subunit, predicted / : / Type I restriction modification DNA specificity domain superfamily / DNA restriction-modification system / DNA binding / Type I restriction-modification system specificty subunit

Function and homology information

Biological species

Streptococcus pyogenes MGAS315 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Muna, T.H. / Prehna, G.

Funding support

Canada, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2025
Title: The phage protein paratox is a multifunctional metabolic regulator of Streptococcus.
Authors: Muna, T.H. / Rutbeek, N.R. / Horne, J. / Lao, Y.W. / Krokhin, O.V. / Prehna, G.

History

Deposition	Jan 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 8, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8vsq.cif.gz	162.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8vsq.ent.gz	125.9 KB	Display	PDB format
PDBx/mmJSON format	8vsq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vsq_validation.pdf.gz	433.5 KB	Display	wwPDB validaton report
Full document	8vsq_full_validation.pdf.gz	437.7 KB	Display
Data in XML	8vsq_validation.xml.gz	17.9 KB	Display
Data in CIF	8vsq_validation.cif.gz	23.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vs/8vsq ftp://data.pdbj.org/pub/pdb/validation_reports/vs/8vsq	HTTPS FTP

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Related structure data

Related structure data	8vsrC C: citing same article (ref.)
Similar structure data	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: Esub1

B: Esub1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	82.362, 43.872, 85.841
Angle α, β, γ (deg.)	90.000, 118.668, 90.000
Int Tables number	3
Space group name H-M	P121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 3 - 198 / Label seq-ID: 3 - 198

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Esub1 Mass: 23574.141 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes MGAS315 (bacteria) Gene: SpyM3_0890 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H2UUU0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.1 Å³/Da / Density % sol: 60.28 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium sulfate 0.1M Tris pH 8.5 40% PEG 400 12 mg/mL protein

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1806 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1806 Å / Relative weight: 1
Reflection	Resolution: 2.9→43.911 Å / Num. obs: 12089 / % possible obs: 99 % / Redundancy: 3.4 % / CC_1/2: 0.999 / R_pim(I) all: 0.043 / R_rim(I) all: 0.08 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.9→3.08 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1931 / CC_1/2: 0.94 / R_pim(I) all: 0.334 / R_rim(I) all: 0.627 / % possible all: 94

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→43.911 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.905 / SU ML: 0.422 / Cross valid method: FREE R-VALUE / ESU R Free: 0.437
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2806	583	4.823 %
R_work	0.2217	11504	-
all	0.224	-	-
obs	-	12087	98.46 %

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_aniso -1	B_aniso -2	B_aniso -3
1-	-5.182 Å²	0 Å²	-1.009 Å²
2-	-	8.04 Å²	0 Å²
3-	-	-	-1.098 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→43.911 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3124	0	5	50	3179

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	3180
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3152
X-RAY DIFFRACTION	r_angle_refined_deg	1.814	1.636	4296
X-RAY DIFFRACTION	r_angle_other_deg	1.272	1.588	7240
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.563	5	390
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.409	22.289	166
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.377	15	594
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.901	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	408
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3546
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	714
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	669
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	3041
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	1517
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	1654
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.021	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.355	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.406	0.2	124
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.472	0.2	5
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.373	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	2.264	4.529	1566
X-RAY DIFFRACTION	r_mcbond_other	2.262	4.529	1564
X-RAY DIFFRACTION	r_mcangle_it	3.539	6.801	1954
X-RAY DIFFRACTION	r_mcangle_other	3.537	6.802	1954
X-RAY DIFFRACTION	r_scbond_it	2.466	4.827	1612
X-RAY DIFFRACTION	r_scbond_other	2.465	4.827	1613
X-RAY DIFFRACTION	r_scangle_it	4.114	7.119	2342
X-RAY DIFFRACTION	r_scangle_other	4.113	7.119	2343
X-RAY DIFFRACTION	r_lrange_it	6.034	52.682	3470
X-RAY DIFFRACTION	r_lrange_other	6.027	52.648	3464
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.039	0.05	6286

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.03877	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.03877	0.0501

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
2.9-2.975	0.346	63	0.372	804	0.37	889	0.57	0.537	97.5253	0.353
2.975-3.057	0.402	41	0.378	819	0.379	875	0.588	0.592	98.2857	0.344
3.057-3.145	0.431	51	0.365	802	0.369	865	0.499	0.594	98.6127	0.338
3.145-3.242	0.272	31	0.295	760	0.294	804	0.818	0.784	98.3831	0.263
3.242-3.348	0.262	39	0.266	755	0.266	810	0.873	0.865	98.0247	0.234
3.348-3.465	0.282	26	0.241	723	0.243	760	0.863	0.87	98.5526	0.202
3.465-3.595	0.313	32	0.248	723	0.251	765	0.837	0.883	98.6928	0.223
3.595-3.742	0.288	27	0.21	691	0.213	727	0.894	0.911	98.762	0.193
3.742-3.908	0.309	33	0.198	644	0.203	683	0.872	0.922	99.1215	0.18
3.908-4.098	0.345	29	0.207	619	0.212	658	0.825	0.919	98.4802	0.183
4.098-4.319	0.216	24	0.158	610	0.16	643	0.946	0.961	98.6003	0.148
4.319-4.58	0.182	29	0.186	562	0.186	598	0.949	0.954	98.8294	0.174
4.58-4.895	0.183	25	0.165	546	0.166	575	0.962	0.954	99.3044	0.156
4.895-5.285	0.346	32	0.187	473	0.194	510	0.885	0.954	99.0196	0.177
5.285-5.787	0.296	21	0.225	464	0.228	490	0.905	0.938	98.9796	0.215
5.787-6.465	0.272	15	0.233	429	0.234	451	0.931	0.938	98.4479	0.217
6.465-7.456	0.266	23	0.222	368	0.224	396	0.929	0.939	98.7374	0.214
7.456-9.11	0.212	16	0.168	311	0.169	334	0.929	0.966	97.9042	0.167
9.11-12.79	0.35	19	0.18	244	0.189	268	0.868	0.965	98.1343	0.197
12.79-75.318	0.195	7	0.259	157	0.255	173	0.947	0.932	94.7977	0.299

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	3.1395	1.3057	1.983	5.0037	2.2566	5.8083	0.2534	-0.0372	-0.019	0.4494	0.0321	-0.8615	0.188	-0.0854	-0.2855	0.1524	0.0606	0.0883	0.5674	0.0357	0.4002	28.095	23.6518	-17.3479
2	5.0427	-1.5093	1.5223	14.3217	-9.3	25.8854	-0.2291	0.302	0.1016	-0.2805	0.0091	-0.4553	-0.8881	1.2005	0.2199	0.4681	0.0415	0.1502	0.569	0.0538	0.7363	36.0658	39.4684	-20.5187
3	1.3895	-0.3386	-1.0619	1.8923	0.4612	3.938	-0.0133	0.1478	0.1163	-0.2	0.0892	-0.5486	-0.0912	0.0314	-0.0759	0.0262	-0.0443	0.054	0.5214	0.0083	0.1627	19.8706	21.7733	-15.1074
4	2.8477	-1.0401	-1.459	5.8271	2.3622	5.05	0.2045	-0.0717	0.096	-0.5134	0.0013	-0.8331	-0.3	-0.0612	-0.2058	0.1312	-0.0471	-0.0726	0.5806	0.027	0.3797	27.7702	18.1439	17.6663
5	0.9462	0.3316	-0.5258	5.8012	-7.6092	11.769	0.2525	-0.2748	-0.0599	0.2464	-0.4952	-0.9595	0.2962	1.2519	0.2427	0.6914	0.0512	-0.2112	0.7229	-0.0846	0.9361	36.0381	1.8263	18.8422
6	4.9923	0.0393	-0.788	3.1061	0.781	3.3001	0.1253	0.0668	-0.1133	0.2368	-0.0804	-1.0602	0.0423	0.0257	-0.0449	0.0747	0.0763	-0.0926	0.5488	0.0035	0.3799	26.4661	20.3866	19.6375
7	0.6719	0.1974	1.51	1.3323	1.354	7.1898	-0.1112	-0.023	-0.0379	0.0662	0.0172	-0.0056	0.1128	-0.3497	0.094	0.1049	0.0007	0.0541	0.3719	0.0164	0.167	10.7455	17.883	8.8477

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	3 - 61
2	X-RAY DIFFRACTION	2	ALL	A	62 - 71
3	X-RAY DIFFRACTION	3	ALL	A	72 - 198
4	X-RAY DIFFRACTION	4	ALL	B	3 - 59
5	X-RAY DIFFRACTION	5	ALL	B	60 - 71
6	X-RAY DIFFRACTION	6	ALL	B	72 - 147
7	X-RAY DIFFRACTION	7	ALL	B	148 - 198

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