[English] 日本語
Yorodumi
- PDB-6zn8: Crystal structure of the H. influenzae VapXD toxin-antitoxin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zn8
TitleCrystal structure of the H. influenzae VapXD toxin-antitoxin complex
Components
  • Endoribonuclease VapD
  • VapX
KeywordsTOXIN / Toxin-antitoxin / VapXD / RNase / Nucleic-Acid Binding Protein / Hydrolase
Function / homology
Function and homology information


nuclease activity / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Protein of unknown function DUF5397 / Family of unknown function (DUF5397) / Endoribonuclease VapD / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2
Similarity search - Domain/homology
VapX / Endoribonuclease VapD
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.211 Å
AuthorsBertelsen, M.B. / Senissar, M. / Nielsen, M.H. / Bisiak, F. / Cunha, M.V. / Molinaro, A.L. / Daines, D.A. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF 120 Denmark
Novo Nordisk FoundationNNF18OC0030646 Denmark
CitationJournal: 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
DepositionJul 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endoribonuclease VapD
B: Endoribonuclease VapD
D: Endoribonuclease VapD
E: Endoribonuclease VapD
C: VapX
F: VapX


Theoretical massNumber of molelcules
Total (without water)65,8426
Polymers65,8426
Non-polymers00
Water00
1
A: Endoribonuclease VapD
B: Endoribonuclease VapD
C: VapX


Theoretical massNumber of molelcules
Total (without water)32,9213
Polymers32,9213
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-21 kcal/mol
Surface area12190 Å2
MethodPISA
2
D: Endoribonuclease VapD
E: Endoribonuclease VapD
F: VapX


Theoretical massNumber of molelcules
Total (without water)32,9213
Polymers32,9213
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-17 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.750, 256.750, 256.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132

-
Components

#1: Protein
Endoribonuclease VapD


Mass: 11915.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria)
Gene: vapD, NTHI0577 / Cell line (production host): B834 (DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: Q4QN95, Hydrolases; Acting on ester bonds
#2: Protein VapX


Mass: 9089.575 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria)
Gene: vapX, NTHI0578 / Cell line (production host): B834 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QN94
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.36 Å3/Da / Density % sol: 77.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M ammonium sulfate, 10% (v/v) 1,4-dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97903 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 3.21→46.88 Å / Num. obs: 23799 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 100.67 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.067 / Rrim(I) all: 0.185 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.21-3.327.61.40723050.5240.5421.513100
12.44-46.885.60.0764680.9950.0330.08496.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
SHELXDEphasing
PHENIX1.18refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.211→46.876 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.2989 2351 9.89 %
Rwork0.2583 --
obs0.2623 23774 99.74 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 154.25 Å2 / Biso mean: 85.5947 Å2 / Biso min: 46.7 Å2
Refinement stepCycle: final / Resolution: 3.211→46.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3939 0 0 0 3939
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014021
X-RAY DIFFRACTIONf_angle_d1.1055440
X-RAY DIFFRACTIONf_chiral_restr0.064593
X-RAY DIFFRACTIONf_plane_restr0.006706
X-RAY DIFFRACTIONf_dihedral_angle_d6.092372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.211-3.27640.40951270.37211262100
3.2764-3.34760.39161290.32071223100
3.3476-3.42550.34741460.30291256100
3.4255-3.51110.32511340.26571218100
3.5111-3.6060.28771370.26721247100
3.606-3.71210.29451380.25731249100
3.7121-3.83180.28251390.2491124999
3.8318-3.96870.28381340.2597121999
3.9687-4.12750.32061390.24281263100
4.1275-4.31530.24891360.21341236100
4.3153-4.54260.29541380.21661255100
4.5426-4.82690.26181390.22261267100
4.8269-5.19920.28781390.2271125399
5.1992-5.72160.29081410.24511276100
5.7216-6.54760.29661420.26111287100
6.5476-8.2420.31491410.29121294100
8.242-46.8760.311520.2909136999

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more