PDB-7e4j: X-ray crystal structure of VapB12 antitoxin from mycobacterium tu...

ID or keywords:

Entry

Database: PDB / ID: 7e4j

Title

X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space group P41.

Components

Antitoxin

Keywords

ANTITOXIN / VapBC12 / Toxin-antitoxin / Cholesterol

Function / homology

: / Antitoxin FitA-like, ribbon-helix-helix / Ribbon-helix-helix / regulation of DNA-templated transcription / Antitoxin

Function and homology information

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 1.63 Å

Authors

Pratap, S. / Megta, A.K. / Talwar, S. / Chandresh, S. / Pandey, A.K. / Krishnan, V.

Citation

Journal: To be published
Title: X-ray crystal structure of VapB12 antitoxin from mycobacterium tuberculosis in space group P41.
Authors: Pratap, S. / Megta, A.K. / Talwar, S. / Sharma, C. / Pandey, A.K. / Krishnan, V.

History

Deposition	Feb 13, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 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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Validation report

Summary document	7e4j_validation.pdf.gz	416.5 KB	Display	wwPDB validaton report
Full document	7e4j_full_validation.pdf.gz	416.5 KB	Display
Data in XML	7e4j_validation.xml.gz	9.2 KB	Display
Data in CIF	7e4j_validation.cif.gz	12.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e4/7e4j ftp://data.pdbj.org/pub/pdb/validation_reports/e4/7e4j	HTTPS FTP

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Related structure data

Similar structure data	7e4j-2 5ilu-d 1j7q-d 1qpm-d 1oay-2 2xsf-d 2uwq-d 3pz8-3 7bnh-1 4j5o-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Antitoxin

B: Antitoxin

C: Antitoxin

D: Antitoxin

hetero molecules

19.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Antitoxin

C: Antitoxin

defined by author&software
Evidence: homology
9.88 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Antitoxin

D: Antitoxin

hetero molecules

defined by author&software
9.95 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	34.660, 34.660, 162.227
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 1 - 44 / Label seq-ID: 1 - 44

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein/peptide	Antitoxin / Antitoxin VapB12 / Conserved protein of uncharacterized function / possible antitoxin VapB12 Mass: 4941.749 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: vapB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, ERS007722_03650, ERS007741_00752, ERS013471_00074, ERS023446_ ...Gene: vapB12, AYJ03_009075, DSI38_08650, E5M52_14165, E5M78_13900, ERS007663_00684, ERS007665_03495, ERS007703_02236, ERS007720_02286, ERS007722_03650, ERS007741_00752, ERS013471_00074, ERS023446_02694, ERS027646_03040, ERS027659_01239, ERS027661_00782, ERS094182_03044, F6W99_00284, FRD82_02990, SAMEA2683035_01359 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A045KH53
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.46 Å³/Da / Density % sol: 50.1 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion / pH: 6.3 Details: 0.2 M Ammonium Chloride:NaOH pH 6.3, 20% (w/v) PEG3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 0.97951 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.97951 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.514
1	1	-K, -H, -L	2	0.486

Reflection

Resolution: 1.63→40.56 Å / Num. obs: 23505 / % possible obs: 99.9 % / Redundancy: 7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.067 / Net I/σ(I): 12.6

Reflection shell

Resolution: 1.635→1.663 Å / Redundancy: 6.3 % / R_merge(I) obs: 0.723 / Mean I/σ(I) obs: 2 / Num. unique obs: 1174 / CC_1/2: 0.806

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Processing

Software

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

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.63→40.56 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.947 / SU B: 3.816 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21794	1106	4.7 %	RANDOM
R_work	0.17177	-	-	-
obs	0.174	22398	99.89 %	-

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: 38.852 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-21.21 Å²	-0 Å²	-0 Å²
2-	-	-21.21 Å²	-0 Å²
3-	-	-	42.41 Å²

Refinement step

Cycle: 1 / Resolution: 1.63→40.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1360	0	1	121	1482

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1382
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	1405
X-RAY DIFFRACTION	r_angle_refined_deg	1.568	1.633	1857
X-RAY DIFFRACTION	r_angle_other_deg	1.273	1.578	3219
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.13	5	172
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.897	20.886	79
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.89	15	266
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.282	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.064	0.2	184
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1524
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	296
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	2.518	3.041	700
X-RAY DIFFRACTION	r_mcbond_other	2.512	3.034	699
X-RAY DIFFRACTION	r_mcangle_it	3.19	4.541	868
X-RAY DIFFRACTION	r_mcangle_other	3.189	4.55	869
X-RAY DIFFRACTION	r_scbond_it	2.909	3.571	682
X-RAY DIFFRACTION	r_scbond_other	2.907	3.578	683
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.8	5.202	990
X-RAY DIFFRACTION	r_long_range_B_refined	4.879	37.496	1508
X-RAY DIFFRACTION	r_long_range_B_other	4.738	37.339	1497
X-RAY DIFFRACTION	r_rigid_bond_restr	4.025	3	2786
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	1183	0.06
1	2	B	1183	0.06
2	1	A	1114	0.14
2	2	C	1114	0.14
3	1	A	1110	0.13
3	2	D	1110	0.13
4	1	B	1110	0.13
4	2	C	1110	0.13
5	1	B	1113	0.13
5	2	D	1113	0.13
6	1	C	1163	0.07
6	2	D	1163	0.07

LS refinement shell

Resolution: 1.635→1.677 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.286	91	-
R_work	0.19	1612	-
obs	-	-	99.59 %

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	1.2849	0.2416	1.9067	0.2151	0.5128	3.456	-0.2	0.1707	0.2434	0.0001	-0.1198	0.0579	-0.0614	0.2492	0.3199	0.1135	-0.0062	-0.0523	0.1814	0.0098	0.0513	16.2503	19.9356	11.076
2	0.0132	0.1001	0.0004	0.8149	-0.0013	0.0006	-0.0062	-0.0016	-0.002	-0.0403	0.0027	-0.0414	0.0017	-0.0014	0.0035	0.0563	-0.0002	0.0057	0.0579	0.0011	0.0161	3.3109	10.8772	8.1223
3	1.1572	0.3394	0.36	0.2844	0.3614	0.4783	0.0247	0.027	-0.0866	0.0229	0.037	-0.0346	0.0418	0.0618	-0.0616	0.0668	0.0117	-0.0087	0.0632	-0.0086	0.0437	13.5469	7.5041	15.3337
4	0.8995	-0.3666	1.661	0.285	-0.9285	4.0355	-0.1049	-0.1082	0.1064	0.0551	0.011	-0.0197	-0.1862	-0.1853	0.094	0.063	0.0055	-0.0049	0.0616	-0.0162	0.0254	1.1757	2.6444	29.0761
5	0.5355	-0.1694	-0.287	0.11	0.0967	0.1568	0.0052	0.0189	0.0093	0.0367	0.0019	-0.0575	0.011	-0.0176	-0.0072	0.081	-0.0004	-0.0218	0.0602	-0.0063	0.057	14.0914	-6.5244	31.9057
6	0.533	-0.4985	0.2497	0.5135	-0.3138	0.2537	-0.0164	0.0135	-0.0276	0.0006	0.0179	0.0181	0.0175	-0.045	-0.0015	0.0632	-0.0066	0.0023	0.0607	-0.0014	0.007	3.8059	-9.7877	24.8382
7	1.8577	-0.8062	2.0612	0.539	-0.4593	3.3026	0.0239	0.087	0.0127	-0.029	-0.0584	0.0037	-0.0041	0.019	0.0346	0.0597	-0.0097	-0.0019	0.0715	0.0019	0.0006	11.8679	19.4031	11.5873
8	0.803	0.043	-0.882	0.5096	-0.0192	0.9722	-0.0207	0.011	-0.0443	0.0197	-0.0249	-0.0036	0.0215	-0.0046	0.0456	0.0392	0.0025	0.0073	0.0548	0.0027	0.0316	25.8361	11.7276	12.9184
9	3.2183	0.015	-0.4902	1.9531	-0.5171	0.211	-0.0264	0.0562	-0.1753	-0.0606	0.0028	0.0176	0.0142	-0.0063	0.0236	0.079	-0.0022	-0.0041	0.0585	-0.0026	0.0101	15.7256	8.8567	5.9822
10	2.1683	0.4414	1.4552	0.4242	-0.3887	2.385	-0.1319	-0.1547	0.157	0.0305	-0.0481	-0.001	-0.2225	-0.0734	0.18	0.0644	0.0232	-0.0171	0.0529	-0.009	0.0516	5.6894	2.1127	28.526
11	0.6722	0.2885	-0.6085	0.1249	-0.2596	0.5532	0.0496	0.0079	0.0532	0.0304	0.0041	0.0196	-0.0332	-0.0094	-0.0537	0.0907	0.0025	-0.0117	0.0549	-0	0.0194	-8.4689	-5.653	27.4934
12	2.6536	0.4694	0.746	0.0833	0.1468	1.1321	0.0291	0.0073	-0.1938	0.0049	-0.0013	-0.0334	-0.0045	0.0433	-0.0277	0.0579	-0.0017	-0.0056	0.061	-0.0088	0.0187	1.5181	-8.4056	34.3229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 11
2	X-RAY DIFFRACTION	2	A	12 - 28
3	X-RAY DIFFRACTION	3	A	29 - 44
4	X-RAY DIFFRACTION	4	B	1 - 11
5	X-RAY DIFFRACTION	5	B	12 - 28
6	X-RAY DIFFRACTION	6	B	29 - 44
7	X-RAY DIFFRACTION	7	C	1 - 11
8	X-RAY DIFFRACTION	8	C	12 - 28
9	X-RAY DIFFRACTION	9	C	29 - 44
10	X-RAY DIFFRACTION	10	D	1 - 11
11	X-RAY DIFFRACTION	11	D	12 - 28
12	X-RAY DIFFRACTION	12	D	29 - 44

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