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- PDB-6zn8: Crystal structure of the H. influenzae VapXD toxin-antitoxin complex -

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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 / homologyProtein of unknown function DUF5397 / Family of unknown function (DUF5397) / Endoribonuclease VapD / nuclease activity / Hydrolases; Acting on ester bonds / RNA binding / VapX / Endoribonuclease VapD
Function and homology information
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water0
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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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