PDB-6zi1: Crystal structure of the isolated H. influenzae VapD toxin (D7N m...

ID or keywords:

Entry

Database: PDB / ID: 6zi1

Title

Crystal structure of the isolated H. influenzae VapD toxin (D7N mutant)

Components

Endoribonuclease VapD

Keywords

TOXIN / Toxin-antitoxin / VapXD / RNase / Nucleic-Acid Binding Protein / Hydrolase

Function / homology

Endoribonuclease VapD / CRISPR associated protein Cas2 / nuclease activity / Hydrolases; Acting on ester bonds / RNA binding / Endoribonuclease VapD

Function and homology information

Biological species

Haemophilus influenzae 86-028NP (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Bertelsen, M.B. / Senissar, M. / Nielsen, M.H. / Bisiak, F. / Cunha, M.V. / Molinaro, A.L. / Daines, D.A. / Brodersen, D.E.

Funding support

Denmark, 1items

Citation

Journal: Structure / Year: 2021
Title: Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System.
Authors: Bertelsen, M.B. / Senissar, M. / Nielsen, M.H. / Bisiak, F. / Cunha, M.V. / Molinaro, A.L. / Daines, D.A. / Brodersen, D.E.

History

Deposition	Jun 24, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 14, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 4, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Feb 17, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6zi1_validation.pdf.gz	436.6 KB	Display	wwPDB validaton report
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Data in CIF	6zi1_validation.cif.gz	12.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zi/6zi1 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zi1	HTTPS FTP

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Related structure data

Related structure data	6zi0C 6zn8C C: citing same article (ref.)
Similar structure data	6sm6-d 5xrw-1 3dvm-d 2v1t-d 2b6m-1 1un2-d 3hdf-1 2ek1-4 6nty-d 2qzb-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Endoribonuclease VapD

BBB: Endoribonuclease VapD

23.7 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)	84.380, 84.380, 49.480
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	AAA-213- HOH
2	1	AAA-219- HOH
3	1	BBB-216- HOH

#1: Protein	Endoribonuclease VapD Mass: 11869.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: D7N mutant Source: (gene. exp.) Haemophilus influenzae 86-028NP (bacteria) Gene: vapD, NTHI0577 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q4QN95, Hydrolases; Acting on ester bonds
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.68 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM Na cacodylate, 1.8 M ammonium sulphate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.98021 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.98021 Å / Relative weight: 1

Reflection

Resolution: 2.2→42.226 Å / Num. obs: 10306 / % possible obs: 97.2 % / Redundancy: 3.334 % / B_iso Wilson estimate: 53.573 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.06 / R_rim(I) all: 0.071 / Χ²: 0.863 / Net I/σ(I): 12.11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.2-2.26	3.096	0.928	1.31	736	0.612	1.122	97.9
2.26-2.32	3.297	0.784	1.41	767	0.638	0.931	98.5
2.32-2.39	3.466	0.607	1.97	721	0.671	0.718	99
2.39-2.46	3.448	0.485	2.37	696	0.781	0.573	99.4
2.46-2.54	3.401	0.466	2.53	689	0.789	0.551	99
2.54-2.63	3.324	0.349	3.2	661	0.866	0.414	99.1
2.63-2.73	3.141	0.277	3.99	644	0.917	0.332	99.5
2.73-2.84	3.231	0.167	6.15	607	0.972	0.199	98.9
2.84-2.97	3.449	0.142	7.49	604	0.983	0.166	98.4
2.97-3.11	3.499	0.106	10.51	551	0.987	0.124	97
3.11-3.28	3.384	0.078	13.9	531	0.994	0.092	97.6
3.28-3.48	3.319	0.059	17.16	504	0.996	0.07	97.1
3.48-3.72	3.124	0.046	21.05	474	0.997	0.055	96.7
3.72-4.02	3.49	0.039	25.99	435	0.998	0.046	95
4.02-4.4	3.465	0.027	34.99	409	0.999	0.031	95.8
4.4-4.92	3.357	0.025	36.81	353	0.999	0.029	92.7
4.92-5.68	3.225	0.026	35.49	320	0.999	0.031	92
5.68-6.96	3.458	0.03	32.22	277	0.999	0.035	93.3
6.96-9.84	3.309	0.022	40.01	207	0.999	0.026	88.5
9.84-42.226	3.067	0.021	49.94	120	0.999	0.024	85.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.2 Å	42.19 Å
Translation	2.2 Å	42.19 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
XSCALE		data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.25	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: D_1292109585

Resolution: 2.2→42.226 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.913 / SU B: 8.908 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / ESU R: 0.31 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2666	1028	9.971 %
R_work	0.2145	9282	-
all	0.22	-	-
obs	-	10306	97.227 %

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: 58.862 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.876 Å²	0.438 Å²	0 Å²
2-	-	0.876 Å²	-0 Å²
3-	-	-	-2.842 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→42.226 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1333	0	0	88	1421

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	1357
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	1242
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.626	1831
X-RAY DIFFRACTION	r_angle_other_deg	1.285	1.574	2846
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.316	5	161
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.923	22.289	83
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.082	15	225
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.103	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	179
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1529
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	329
X-RAY DIFFRACTION	r_nbd_refined	0.257	0.2	329
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	1311
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	661
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	716
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.226	0.2	85
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.348	0.2	45
X-RAY DIFFRACTION	r_nbd_other	0.296	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.218	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	4.931	5.858	656
X-RAY DIFFRACTION	r_mcbond_other	4.931	5.849	655
X-RAY DIFFRACTION	r_mcangle_it	7.78	8.721	813
X-RAY DIFFRACTION	r_mcangle_other	7.778	8.731	814
X-RAY DIFFRACTION	r_scbond_it	5.796	6.586	699
X-RAY DIFFRACTION	r_scbond_other	5.773	6.575	697
X-RAY DIFFRACTION	r_scangle_it	9.149	9.665	1018
X-RAY DIFFRACTION	r_scangle_other	9.134	9.666	1018
X-RAY DIFFRACTION	r_lrange_it	17.508	108.489	5237
X-RAY DIFFRACTION	r_lrange_other	17.478	108.318	5193

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2-2.257	0.409	68	0.386	668	X-RAY DIFFRACTION	97.8723
2.257-2.319	0.365	82	0.329	684	X-RAY DIFFRACTION	98.9664
2.319-2.386	0.359	73	0.304	647	X-RAY DIFFRACTION	99.0371
2.386-2.459	0.302	75	0.265	627	X-RAY DIFFRACTION	99.4334
2.459-2.54	0.333	75	0.256	606	X-RAY DIFFRACTION	98.9826
2.54-2.629	0.293	64	0.237	605	X-RAY DIFFRACTION	99.1111
2.629-2.728	0.259	68	0.242	570	X-RAY DIFFRACTION	99.532
2.728-2.839	0.314	57	0.223	554	X-RAY DIFFRACTION	98.8673
2.839-2.965	0.252	55	0.208	546	X-RAY DIFFRACTION	98.3633
2.965-3.11	0.265	58	0.195	486	X-RAY DIFFRACTION	96.9697
3.11-3.278	0.212	51	0.199	492	X-RAY DIFFRACTION	97.6619
3.278-3.476	0.311	43	0.209	454	X-RAY DIFFRACTION	97.0703
3.476-3.716	0.266	45	0.201	430	X-RAY DIFFRACTION	96.7413
3.716-4.012	0.21	45	0.163	390	X-RAY DIFFRACTION	94.9782
4.012-4.394	0.3	38	0.147	371	X-RAY DIFFRACTION	96.0094
4.394-4.911	0.183	33	0.163	323	X-RAY DIFFRACTION	92.4675
4.911-5.666	0.189	34	0.216	286	X-RAY DIFFRACTION	92.219
5.666-6.929	0.348	28	0.256	241	X-RAY DIFFRACTION	92.7586
6.929-9.755	0.198	23	0.239	190	X-RAY DIFFRACTION	89.1213
9.755-42.226	0.38	13	0.275	112	X-RAY DIFFRACTION	85.034

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