PDB-7vwo: TA complex from Mycobacterium tuberculosis

ID or keywords:

Entry

Database: PDB / ID: 7vwo

Title

TA complex from Mycobacterium tuberculosis

Components

Antitoxin VapB43
Ribonuclease VapC43

Keywords

TOXIN/ANTITOXIN / Toxin-Antitoxin complex Ribonuclease / TOXIN / TOXIN-ANTITOXIN complex

Function / homology

Function and homology information

positive regulation of growth / negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / regulation of DNA-templated transcription / magnesium ion binding / plasma membrane
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Eun, H.-J. / Lee, B.-J. / Lee, J.-Y.

Funding support

Korea, Republic Of, 3items

Organization	Grant number	Country
National Research Foundation (NRF, Korea)	2018R1A5A2024425	Korea, Republic Of
National Research Foundation (NRF, Korea)	2021R1F1A1050961	Korea, Republic Of
National Research Foundation (NRF, Korea)	2021 BK21 Plus Project for Medicine, Dentistry and Pharmacy	Korea, Republic Of

Citation

Journal: To Be Published
Title: TA complex from Mycobacterium tuberculosis
Authors: Eun, H.-J. / Lee, B.-J. / Lee, J.-Y.

History

Deposition	Nov 11, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vwo.cif.gz	386.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7vwo.ent.gz	316.8 KB	Display	PDB format
PDBx/mmJSON format	7vwo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vwo_validation.pdf.gz	486.5 KB	Display	wwPDB validaton report
Full document	7vwo_full_validation.pdf.gz	497.1 KB	Display
Data in XML	7vwo_validation.xml.gz	40.4 KB	Display
Data in CIF	7vwo_validation.cif.gz	58.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vw/7vwo ftp://data.pdbj.org/pub/pdb/validation_reports/vw/7vwo	HTTPS FTP

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Related structure data

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
Related items in Molecule of the Month	#3 - Mar 2000 DNA Polymerase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

A: Ribonuclease VapC43

B: Ribonuclease VapC43

E: Ribonuclease VapC43

K: Ribonuclease VapC43

I: Ribonuclease VapC43

G: Ribonuclease VapC43

H: Antitoxin VapB43

D: Antitoxin VapB43

J: Antitoxin VapB43

105 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribonuclease VapC43

B: Ribonuclease VapC43

D: Antitoxin VapB43

defined by author&software
Evidence: gel filtration
35 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Ribonuclease VapC43

G: Ribonuclease VapC43

H: Antitoxin VapB43

defined by author&software
35 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

K: Ribonuclease VapC43

I: Ribonuclease VapC43

J: Antitoxin VapB43

defined by author&software
35 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.847, 74.501, 74.882
Angle α, β, γ (deg.)	73.16, 70.24, 70.03
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ASP	ASP	A	A	1 - 142	1 - 142
2	1	MET	MET	ASP	ASP	B	B	1 - 142	1 - 142
1	2	MET	MET	ASP	ASP	A	A	1 - 142	1 - 142
2	2	MET	MET	ASP	ASP	E	C	1 - 142	1 - 142
1	3	MET	MET	ASP	ASP	A	A	1 - 142	1 - 142
2	3	MET	MET	ASP	ASP	K	D	1 - 142	1 - 142
1	4	MET	MET	ASP	ASP	A	A	1 - 142	1 - 142
2	4	MET	MET	ASP	ASP	I	E	1 - 142	1 - 142
1	5	MET	MET	ASP	ASP	A	A	1 - 142	1 - 142
2	5	MET	MET	ASP	ASP	G	F	1 - 142	1 - 142
1	6	MET	MET	ASP	ASP	B	B	1 - 142	1 - 142
2	6	MET	MET	ASP	ASP	E	C	1 - 142	1 - 142
1	7	MET	MET	ASP	ASP	B	B	1 - 142	1 - 142
2	7	MET	MET	ASP	ASP	K	D	1 - 142	1 - 142
1	8	MET	MET	ASP	ASP	B	B	1 - 142	1 - 142
2	8	MET	MET	ASP	ASP	I	E	1 - 142	1 - 142
1	9	MET	MET	ASP	ASP	B	B	1 - 142	1 - 142
2	9	MET	MET	ASP	ASP	G	F	1 - 142	1 - 142
1	10	MET	MET	ASP	ASP	E	C	1 - 142	1 - 142
2	10	MET	MET	ASP	ASP	K	D	1 - 142	1 - 142
1	11	MET	MET	ASP	ASP	E	C	1 - 142	1 - 142
2	11	MET	MET	ASP	ASP	I	E	1 - 142	1 - 142
1	12	MET	MET	ASP	ASP	E	C	1 - 142	1 - 142
2	12	MET	MET	ASP	ASP	G	F	1 - 142	1 - 142
1	13	MET	MET	ASP	ASP	K	D	1 - 142	1 - 142
2	13	MET	MET	ASP	ASP	I	E	1 - 142	1 - 142
1	14	MET	MET	ASP	ASP	K	D	1 - 142	1 - 142
2	14	MET	MET	ASP	ASP	G	F	1 - 142	1 - 142
1	15	MET	MET	ASP	ASP	I	E	1 - 142	1 - 142
2	15	MET	MET	ASP	ASP	G	F	1 - 142	1 - 142
1	16	TYR	TYR	ASN	ASN	H	G	1 - 28	1 - 28
2	16	TYR	TYR	ASN	ASN	D	H	1 - 28	1 - 28
1	17	TYR	TYR	ASN	ASN	H	G	1 - 28	1 - 28
2	17	TYR	TYR	ASN	ASN	J	I	1 - 28	1 - 28
1	18	TYR	TYR	ASN	ASN	D	H	1 - 28	1 - 28
2	18	TYR	TYR	ASN	ASN	J	I	1 - 28	1 - 28

NCS ensembles :

#1: Protein	Ribonuclease VapC43 / RNase VapC43 / Toxin VapC43 Mass: 16081.110 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: vapC43, Rv2872, MTCY274.03 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: P9WF55, Hydrolases; Acting on ester bonds
#2: Protein/peptide	Antitoxin VapB43 Mass: 2862.205 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: vapB43, Rv2871, MTCY274.02 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P9WL41
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium chloride, 0.1 M Magnesium acetate tetrahydrate 0.05 M Sodium cacodylate trihydrate pH 6.5 10% w/v Polyethylene glycol 8,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→44.55 Å / Num. obs: 59128 / % possible obs: 95.67 % / Redundancy: 2 % / CC_1/2: 0.996 / R_merge(I) obs: 0.048 / R_pim(I) all: 0.042 / R_rim(I) all: 0.064 / Net I/σ(I): 5.1
Reflection shell	Resolution: 1.8→1.86 Å / Num. unique obs: 8216 / CC_1/2: 0.323

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→44.55 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.936 / SU B: 12.045 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24685	2962	4.8 %	RANDOM
R_work	0.2014	-	-	-
obs	0.2036	59128	96.36 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 48.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.1 Å²	0.68 Å²	-1.23 Å²
2-	-	-0.8 Å²	0.2 Å²
3-	-	-	0.56 Å²

Refinement step

Cycle: 1 / Resolution: 2→44.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7388	0	0	618	8006

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.013	7563
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.014	7089
X-RAY DIFFRACTION	r_angle_refined_deg	1.936	1.638	10290
X-RAY DIFFRACTION	r_angle_other_deg	1.469	1.586	16098
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.023	5	927
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.512	19.593	516
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.05	15	1146
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.681	15	108
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	924
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	8793
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1995
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.858	3.007	3735
X-RAY DIFFRACTION	r_mcbond_other	2.858	3.008	3734
X-RAY DIFFRACTION	r_mcangle_it	3.676	4.494	4653
X-RAY DIFFRACTION	r_mcangle_other	3.676	4.493	4654
X-RAY DIFFRACTION	r_scbond_it	3.606	3.497	3828
X-RAY DIFFRACTION	r_scbond_other	3.605	3.496	3829
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.28	5.071	5638
X-RAY DIFFRACTION	r_long_range_B_refined	9.122	38.1	8873
X-RAY DIFFRACTION	r_long_range_B_other	9.083	37.509	8755
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	4542	0.09
1	2	B	4542	0.09
2	1	A	4505	0.1
2	2	E	4505	0.1
3	1	A	4503	0.1
3	2	K	4503	0.1
4	1	A	4500	0.09
4	2	I	4500	0.09
5	1	A	4611	0.07
5	2	G	4611	0.07
6	1	B	4606	0.08
6	2	E	4606	0.08
7	1	B	4478	0.1
7	2	K	4478	0.1
8	1	B	4505	0.09
8	2	I	4505	0.09
9	1	B	4523	0.1
9	2	G	4523	0.1
10	1	E	4463	0.1
10	2	K	4463	0.1
11	1	E	4468	0.09
11	2	I	4468	0.09
12	1	E	4523	0.09
12	2	G	4523	0.09
13	1	K	4592	0.07
13	2	I	4592	0.07
14	1	K	4492	0.1
14	2	G	4492	0.1
15	1	I	4511	0.09
15	2	G	4511	0.09
16	1	H	578	0.15
16	2	D	578	0.15
17	1	H	566	0.17
17	2	J	566	0.17
18	1	D	565	0.16
18	2	J	565	0.16

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	198	-
R_work	0.276	4309	-
obs	-	-	95.37 %

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	3.3491	-0.5923	0.1669	2.5832	-0.036	1.9752	-0.0718	-0.1107	0.3172	0.1741	0.1517	0.0574	-0.1134	0.0101	-0.0799	0.1641	0.0186	0.0721	0.0113	-0.0013	0.0698	3.552	5.7041	9.8111
2	2.9828	-0.7989	1.4015	2.3855	-0.0789	2.3252	-0.0352	0.2939	-0.1043	-0.2268	0.1583	0.2457	-0.0046	0.0235	-0.1231	0.1456	-0.03	0.0411	0.111	0.0468	0.0805	-5.6948	-7.0609	-7.2889
3	2.949	0.4965	-0.9592	2.092	-0.0115	2.1724	-0.0717	-0.2806	0.0944	0.2312	0.1943	0.187	0.0612	-0.0667	-0.1226	0.138	0.0537	0.0471	0.1132	0.0525	0.0494	19.6802	-24.0685	16.32
4	0.8558	-0.0485	0.1034	3.6228	-0.8182	2.7983	0.1797	0.0457	-0.1697	-0.249	-0.1373	0.0307	0.3543	-0.0507	-0.0425	0.112	0.0012	-0.0097	0.1517	0.029	0.0787	16.4912	-33.8556	-32.8661
5	0.9918	0.2216	0.0518	4.042	-0.7565	3.2037	0.1534	-0.0526	0.1412	0.304	-0.1606	-0.0487	-0.3784	-0.052	0.0072	0.1327	0.0107	0.0714	0.1308	0.0275	0.0752	16.401	-11.0389	-27.1354
6	3.4445	0.5895	-0.0952	2.7184	0.1852	1.976	-0.0152	0.1256	-0.3206	-0.2093	0.1366	0.0628	0.177	0.0095	-0.1213	0.1519	0.0088	0.0075	0.0158	0.0008	0.055	29.0549	-36.7748	-0.7294
7	3.5315	0.9936	0.6571	2.3491	-0.314	2.8774	0.0952	-0.0714	-0.2767	0.129	0.018	-0.3295	0.1134	0.2398	-0.1132	0.3035	0.0728	-0.0012	0.1765	-0.0227	0.2791	39.6704	-38.8079	6.3597
8	3.3477	-0.3998	0.2563	2.1263	-0.4976	3.0416	-0.061	0.1464	0.512	0.0072	0.0093	-0.3197	-0.1853	0.3345	0.0517	0.3507	-0.0232	0.1262	0.2067	0.0251	0.2468	14.0757	7.733	2.7531
9	3.6733	-1.648	2.3282	1.0777	-1.1605	1.9884	0.1865	-0.2393	0.0271	-0.0504	0.0215	0.3918	-0.18	-0.5528	-0.208	0.4111	0.1178	0.1339	0.4916	-0.0464	0.5032	5.4367	-8.9477	-33.1433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 142
2	X-RAY DIFFRACTION	2	B	1 - 142
3	X-RAY DIFFRACTION	3	E	1 - 142
4	X-RAY DIFFRACTION	4	K	1 - 142
5	X-RAY DIFFRACTION	5	I	1 - 142
6	X-RAY DIFFRACTION	6	G	1 - 142
7	X-RAY DIFFRACTION	7	H	1 - 28
8	X-RAY DIFFRACTION	8	D	1 - 28
9	X-RAY DIFFRACTION	9	J	1 - 28

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