PDB-6zi0: Crystal structure of the isolated H. influenzae VapD toxin (wildtype)

ID or keywords:

Entry

Database: PDB / ID: 6zi0

Title

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

Components

Endoribonuclease VapD

Keywords

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

Function / homology

Endoribonuclease VapD / Virulence-associated protein D / CRISPR associated protein Cas2 / 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 / Resolution: 2.5 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 Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Feb 17, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3	Jan 31, 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

-
Download

PDBx/mmCIF format	6zi0.cif.gz	35.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6zi0.ent.gz		Display	PDB format
PDBx/mmJSON format	6zi0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6zi0_validation.pdf.gz	429.7 KB	Display	wwPDB validaton report
Full document	6zi0_full_validation.pdf.gz	431.1 KB	Display
Data in XML	6zi0_validation.xml.gz	6.4 KB	Display
Data in CIF	6zi0_validation.cif.gz	7.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zi/6zi0 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/6zi0	HTTPS FTP

-
Related structure data

Related structure data	6zi1C 6zn8C 6hkd PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4n2y-5 3x0g-1 3w8g-d 6h5u-2 6gp6-d 2n82-d 4n2y-4 3akd-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

AAA: Endoribonuclease VapD

11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Endoribonuclease VapD

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

Unit cell

Length a, b, c (Å)	99.100, 99.100, 44.470
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22

Components on special symmetry positions

ID	Model	Components
1	1	AAA-207- HOH
2	1	AAA-219- HOH
3	1	AAA-222- HOH
4	1	AAA-253- HOH

#1: Protein	Endoribonuclease VapD Mass: 11870.337 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source 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.: 55 / 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: 2.66 Å³/Da / Density % sol: 53.68 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1 M LiCl, 0.1 M citrate, 20% PEG 6000

-
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: Mar 22, 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: 2.5→85.882 Å / Num. obs: 4800 / % possible obs: 99.9 % / Redundancy: 10.357 % / B_iso Wilson estimate: 44.739 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.212 / R_rim(I) all: 0.223 / Χ²: 0.785 / Net I/σ(I): 9.49

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
2.5-2.56	10.677	1.581	1.33	344	0.546	1.659	100
2.56-2.64	11.162	1.623	1.33	333	0.527	1.701	99.7
2.64-2.71	11.031	1.335	1.7	325	0.608	1.401	100
2.71-2.8	10.81	0.947	2.33	321	0.71	0.993	100
2.8-2.89	10.579	0.71	3.05	304	0.859	0.745	100
2.89-2.99	10.336	0.586	3.78	298	0.881	0.617	100
2.99-3.1	9.639	0.54	3.9	291	0.908	0.57	99.7
3.1-3.23	10.957	0.422	5.49	276	0.97	0.442	100
3.23-3.37	10.85	0.292	7.18	266	0.972	0.306	100
3.37-3.54	10.562	0.225	9.58	260	0.986	0.236	100
3.54-3.73	10.474	0.162	12.54	249	0.989	0.171	100
3.73-3.95	9.803	0.13	14.85	233	0.992	0.137	100
3.95-4.23	9.909	0.11	16.64	220	0.995	0.116	100
4.23-4.56	10.659	0.089	21.44	211	0.997	0.093	100
4.56-5	10.434	0.079	23.19	196	0.997	0.083	100
5-5.59	9.713	0.096	19.58	181	0.997	0.101	99.5
5.59-6.46	9.217	0.118	16.4	161	0.995	0.125	100
6.46-7.91	9.862	0.083	20.17	138	0.997	0.088	100
7.91-11.18	8.504	0.041	31.7	119	0.999	0.044	100
11.18-85.882	7.189	0.036	29.4	74	1	0.038	98.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
MxCuBE		data collection
XDS		data reduction
PHASER		phasing
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6HKD

6hkd
PDB Unreleased entry

Resolution: 2.5→85.882 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.908 / SU B: 11.962 / SU ML: 0.245 / Cross valid method: FREE R-VALUE / ESU R: 0.41 / ESU R Free: 0.277
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2636	241	5.02 %
R_work	0.2202	4560	-
all	0.222	-	-
obs	-	4800	99.917 %

Solvent computation

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

Displacement parameters

B_iso mean: 76.248 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.869 Å²	0.435 Å²	0 Å²
2-	-	0.869 Å²	0 Å²
3-	-	-	-2.821 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→85.882 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	722	0	0	55	777

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	737
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	662
X-RAY DIFFRACTION	r_angle_refined_deg	1.741	1.633	997
X-RAY DIFFRACTION	r_angle_other_deg	1.24	1.58	1527
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.513	5	89
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.995	23.256	43
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.109	15	122
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	25.709	15	4
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	96
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	836
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	168
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	136
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	603
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	323
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	358
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.201	0.2	24
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.255	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.238	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.256	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	6.859	7.842	359
X-RAY DIFFRACTION	r_mcbond_other	6.646	7.838	358
X-RAY DIFFRACTION	r_mcangle_it	9.803	11.72	447
X-RAY DIFFRACTION	r_mcangle_other	9.815	11.735	448
X-RAY DIFFRACTION	r_scbond_it	7.744	8.593	377
X-RAY DIFFRACTION	r_scbond_other	7.435	8.58	375
X-RAY DIFFRACTION	r_scangle_it	11.133	12.603	550
X-RAY DIFFRACTION	r_scangle_other	11.13	12.612	550
X-RAY DIFFRACTION	r_lrange_it	16.647	147.271	2817
X-RAY DIFFRACTION	r_lrange_other	16.564	147.192	2796

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
2.5-2.565	0.289	18	0.284	326	0.285	344	0.809	0.802	100	0.275
2.565-2.635	0.406	16	0.296	317	0.301	333	0.763	0.776	100	0.289
2.635-2.711	0.27	17	0.297	307	0.296	324	0.765	0.8	100	0.288
2.711-2.795	0.298	16	0.279	307	0.28	323	0.765	0.835	100	0.251
2.795-2.886	0.23	15	0.255	288	0.254	303	0.86	0.863	100	0.222
2.886-2.988	0.291	15	0.234	283	0.237	298	0.864	0.894	100	0.202
2.988-3.1	0.328	14	0.228	277	0.233	292	0.871	0.884	99.6575	0.199
3.1-3.227	0.32	14	0.214	263	0.219	277	0.875	0.909	100	0.187
3.227-3.37	0.35	13	0.203	252	0.21	265	0.881	0.923	100	0.162
3.37-3.534	0.255	13	0.2	248	0.202	261	0.927	0.937	100	0.169
3.534-3.725	0.176	13	0.189	235	0.188	248	0.93	0.946	100	0.162
3.725-3.95	0.255	12	0.193	220	0.196	232	0.957	0.944	100	0.165
3.95-4.222	0.305	10	0.19	210	0.194	220	0.892	0.953	100	0.159
4.222-4.56	0.174	11	0.162	200	0.163	211	0.958	0.966	100	0.137
4.56-4.994	0.266	10	0.176	186	0.181	196	0.938	0.963	100	0.155
4.994-5.581	0.162	9	0.209	174	0.207	184	0.935	0.952	99.4565	0.175
5.581-6.439	0.444	8	0.259	150	0.267	158	0.872	0.929	100	0.232
6.439-7.876	0.346	7	0.256	133	0.262	140	0.907	0.936	100	0.232
7.876-11.091	0.18	6	0.217	113	0.215	119	0.987	0.965	100	0.206
11.091-85.882	0.219	4	0.363	70	0.356	75	0.964	0.929	98.6667	0.358

-
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://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

-
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

-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

-
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