PDB-5wz4: Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c),...

ID or keywords:

Entry

Database: PDB / ID: 5wz4

Title

Crystal structure of Mycobacterium tuberculosis VapC20 (Rv2549c), Sarcin-Ricin loop cleaving toxin

Components

23S rRNA-specific endonuclease VapC20

Keywords

HYDROLASE / VapC toxin / Toxin-antitoxin system / Sarcin-Ricin loop cleaving toxin / Pin-domain / Homodimer

Function / homology

Function and homology information

modulation by symbiont of host process / rRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.775 Å

Authors

Thakur, K.G. / Deep, A.

Funding support

India, 2items

Citation

Journal: FEBS J. / Year: 2017
Title: Crystal structure of Mycobacterium tuberculosis VapC20 toxin and its interactions with cognate antitoxin, VapB20, suggest a model for toxin-antitoxin assembly.
Authors: Deep, A. / Kaundal, S. / Agarwal, S. / Singh, R. / Thakur, K.G.

History

Deposition	Jan 17, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Apr 11, 2018	Group: Data collection / Database references / Source and taxonomy Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3	Mar 1, 2023	Group: Database references / Source and taxonomy / Category: database_2 / entity_src_gen Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5wz4.cif.gz	114.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5wz4.ent.gz	91.4 KB	Display	PDB format
PDBx/mmJSON format	5wz4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5wz4_validation.pdf.gz	433.7 KB	Display	wwPDB validaton report
Full document	5wz4_full_validation.pdf.gz	434.6 KB	Display
Data in XML	5wz4_validation.xml.gz	14.2 KB	Display
Data in CIF	5wz4_validation.cif.gz	20.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wz/5wz4 ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wz4	HTTPS FTP

-
Related structure data

Related structure data	5wzfC C: citing same article (ref.)
Similar structure data	5wzf-d 2a3u-d 3n31-d 3ni9-1 6afn-d 5x5m-2 6h1i-d 2zqa-d 6yrs-2 3his-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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: 23S rRNA-specific endonuclease VapC20

B: 23S rRNA-specific endonuclease VapC20

32.4 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)	48.820, 59.280, 78.620
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	23S rRNA-specific endonuclease VapC20 / Ribonuclease VapC20 / RNase VapC20 / Toxin VapC20 Mass: 16185.639 Da / Num. of mol.: 2 / Mutation: D5A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: vapC20, Rv2549c / Production host: Escherichia coli (E. coli) References: UniProt: P95004, UniProt: P0DMV7*PLUS, Hydrolases; Acting on ester bonds
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

23S rRNA-specific endonuclease VapC20 / Ribonuclease VapC20 / RNase VapC20 / Toxin VapC20

Mass: 16185.639 Da / Num. of mol.: 2 / Mutation: D5A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis H37Rv (bacteria)
Gene: vapC20, Rv2549c / Production host:

Escherichia coli (E. coli)
References: UniProt: P95004, UniProt: P0DMV7*PLUS, Hydrolases; Acting on ester bonds

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.77 Å³/Da / Density % sol: 30.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

RRCAT INDUS-2

/ Beamline: PX-BL21 / Wavelength: 0.97885 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97885 Å / Relative weight: 1

Reflection

Resolution: 1.775→78.62 Å / Num. all: 22721 / Num. obs: 22721 / % possible obs: 99.9 % / Redundancy: 4.3 % / R_pim(I) all: 0.06 / R_rim(I) all: 0.128 / R_sym value: 0.092 / Net I/av σ(I): 6.3 / Net I/σ(I): 7.5 / Num. measured all: 98358

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	R_pim(I) all	R_rim(I) all	R_sym value	% possible all
1.78-1.87	4.3	0.601	1.1	0.383	0.802	0.601	100
1.87-1.98	4.4	0.395	1.8	0.25	0.527	0.395	100
1.98-2.12	4.4	0.248	3	0.156	0.33	0.248	100
2.12-2.29	4.4	0.159	4.3	0.102	0.215	0.159	100
2.29-2.51	4.4	0.124	5.6	0.081	0.172	0.124	100
2.51-2.81	4.4	0.084	8.5	0.058	0.123	0.084	100
2.81-3.24	4.4	0.06	11.2	0.041	0.087	0.06	100
3.24-3.97	4.3	0.061	9.2	0.038	0.081	0.061	100
3.97-5.61	4.2	0.049	11.7	0.033	0.069	0.049	100
5.61-18.324	3.8	0.031	16.1	0.026	0.055	0.031	97.2

-
Phasing

Phasing	Method: SAD

-
Processing

Software

Name	Version	Classification
MOSFLM	0.5.8	data collection
SCALA	3.3.22	data scaling
SOLVE		phasing
RESOLVE		phasing
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.22	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.775→18.317 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 20.2

	R_factor	Num. reflection	% reflection
R_free	0.212	1058	4.93 %
R_work	0.1747	-	-
obs	0.1765	21466	94.66 %

Solvent computation

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

Displacement parameters

B_iso max: 69.32 Å² / B_iso mean: 17.5618 Å² / B_iso min: 3.17 Å²

Refinement step

Cycle: final / Resolution: 1.775→18.317 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2038	0	0	272	2310
B_iso mean	-	-	-	28.61	-
Num. residues	-	-	-	-	260

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2123
X-RAY DIFFRACTION	f_angle_d	0.683	2889
X-RAY DIFFRACTION	f_chiral_restr	0.032	314
X-RAY DIFFRACTION	f_plane_restr	0.003	371
X-RAY DIFFRACTION	f_dihedral_angle_d	15.392	741

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 8

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.775-1.8557	0.3203	125	0.2841	2238	2363	85
1.8557-1.9535	0.284	132	0.2399	2330	2462	88
1.9535-2.0757	0.2513	129	0.1936	2496	2625	94
2.0757-2.2357	0.2324	139	0.1734	2546	2685	96
2.2357-2.4602	0.2135	120	0.1696	2622	2742	97
2.4602-2.8151	0.1981	130	0.1732	2652	2782	98
2.8151-3.5425	0.21	130	0.1618	2697	2827	99
3.5425-18.3175	0.1612	153	0.145	2827	2980	99

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	-0	-0.0015	0.0004	0.0061	0.0043	0.0003	-0.0306	-0.047	0.0529	0.0371	0.0385	-0.0189	-0.0704	-0.1068	0.0098	0.1505	0.0514	-0.0203	0.1447	-0.0114	0.1173	22.0013	40.9118	71.437
2	0.1458	0.0727	0.0099	0.0541	-0.0472	0.2362	-0.0412	-0.0262	-0.0443	0.0991	0.0413	0.0064	0.176	-0.0792	0.0836	0.0949	-0.0171	0.0361	0.0807	0.0032	0.084	22.4374	26.3912	67.8455
3	0.02	0.0003	0.0061	0.0006	0.0018	0.0025	-0.0019	-0.0208	0.0053	-0.012	-0.0223	-0.0418	-0.0046	0.0034	-0.0048	0.0425	0.0028	0.012	0.0814	-0.0123	0.0568	34.5979	33.5215	64.7003
4	0.017	-0.0068	0.0411	0.018	-0.0374	0.1305	0.0343	-0.1549	0.1339	0.0816	0.0946	0.0466	0.0276	-0.0269	0.0421	0.1062	-0.0073	0.0336	0.132	-0.0566	0.1418	35.2482	38.2105	69.773
5	0.0139	0.0158	0.0043	0.0068	-0.0052	0.01	-0.0161	-0.0218	-0.1325	0.0947	-0.0256	-0.0358	0.0276	-0.0041	0	0.1494	-0.0024	0.0058	0.1065	-0.0024	0.1044	31.6862	20.5996	65.031
6	0.0071	-0.006	0.0016	0.0056	0.0024	0.004	0.0138	0.0626	-0.0606	-0.0638	0.0997	0.066	0.0373	-0.0166	0.0174	0.078	-0.0152	-0.0023	0.0904	-0.0181	0.0641	29.899	24.9476	46.8231
7	0.0298	-0.0082	0.0233	0.0068	-0.0176	0.0291	-0.0292	0.192	0.1338	-0.0378	-0.0359	0.1238	-0.0292	-0.0856	-0.0111	0.0552	0.0155	-0.0149	0.0914	0.0074	0.0962	25.5594	32.3824	48.2131
8	0.0318	-0.0279	0.0146	0.0354	-0.0038	0.0141	-0.004	0.0113	-0.0786	0.0372	0.0443	0.0628	0.0392	-0.073	0.0191	-0.1544	-0.134	0.0669	0.0216	0.0123	0.0772	23.422	22.9304	55.1275
9	0.0321	0.0047	0.0316	0.0181	0.0311	0.0658	-0.0496	-0.0497	-0.0788	-0.005	-0.0312	0.0463	-0.0515	0.0291	-0.0099	0.0548	-0.0132	0.008	0.1171	-0.0025	0.1024	18.8758	29.4958	59.8465
10	0.0063	0.0075	0.0004	0.0067	0.0025	0.02	0.0063	0.0514	0.0169	0.0449	0.0304	0.0078	-0.0346	-0.019	0.0022	0.0367	0.0252	0.0029	0.2406	-0.009	0.0901	14.7909	31.8156	58.803
11	0.0279	-0.0147	0.0352	0.0111	-0.0256	0.0619	-0.1852	0.1149	0.141	-0.062	0.0177	-0.1012	-0.1336	0.1404	-0.0051	0.1712	-0.0463	-0.0004	0.0524	0.0178	0.1305	49.8264	41.5874	42.2845
12	0.0039	0.0041	-0.0095	0.0366	-0.0114	0.0534	0.0379	0.0288	-0.0533	0.0038	-0.0059	-0.0499	0.1436	0.0833	0.0117	0.0797	0.0049	0.0011	0.0292	0.0112	0.0468	44.4833	29.2919	50.5228
13	0.1026	0.0676	0.0167	0.0575	0.0116	0.0201	-0.0657	0.1225	0.0939	-0.0656	0.1173	-0.0324	-0.1371	-0.0789	0.007	0.0857	0.0401	-0.0194	0.0513	0.0053	0.0668	34.3022	37.1485	44.3022
14	0.0453	-0.0122	-0.005	0.0255	0.0261	0.0396	-0.0452	-0.0682	-0.1061	0.0299	-0.0075	-0.092	0.1494	0.0561	-0.0073	0.1051	-0.0006	0.0204	0.1092	0.0067	0.0629	44.2184	25.1399	57.4065
15	0.0214	0.015	0.0139	0.0152	0.0102	0.0274	0.021	-0.1475	0.1586	0.0225	0.0268	-0.0216	0.0066	0.0587	0.0007	0.067	-0.0165	-0.0033	0.1251	-0.0844	0.1205	45.6107	36.3526	65.7301
16	0.0343	0.0011	-0.0237	0.0598	-0.0062	0.0915	-0.0734	-0.024	-0.022	0.045	0.0376	0.0174	-0.0543	0.0209	-0.051	0.0361	-0.0066	-0.0093	0.0265	-0.0219	0.0625	53.3933	34.5503	56.1875

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 24 )	A	13 - 24
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 40 )	A	25 - 40
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 41 through 45 )	A	41 - 45
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 46 through 63 )	A	46 - 63
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 64 through 77 )	A	64 - 77
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 78 through 87 )	A	78 - 87
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 88 through 100 )	A	88 - 100
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 101 through 107 )	A	101 - 107
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 108 through 120 )	A	108 - 120
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 121 through 130 )	A	121 - 130
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 12 through 31 )	B	12 - 31
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 32 through 44 )	B	32 - 44
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 45 through 63 )	B	45 - 63
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 64 through 87 )	B	64 - 87
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 88 through 100 )	B	88 - 100
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 101 through 130 )	B	101 - 130

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi