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- PDB-8fzy: Bacteroides spp. Ntox15 domain type VI secretion system effector Tde1 -

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Basic information

Entry
Database: PDB / ID: 8fzy
TitleBacteroides spp. Ntox15 domain type VI secretion system effector Tde1
ComponentsNtox15 domain-containing protein
KeywordsTOXIN / type VI secretion system / effector / DNAse / nuclease
Biological speciesBacteroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBosch, D.E. / Mougous, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K08 AI159619 United States
CitationJournal: Mbio / Year: 2023
Title: Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.
Authors: Bosch, D.E. / Abbasian, R. / Parajuli, B. / Peterson, S.B. / Mougous, J.D.
History
DepositionJan 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ntox15 domain-containing protein
B: Ntox15 domain-containing protein
C: Ntox15 domain-containing protein
D: Ntox15 domain-containing protein
E: Ntox15 domain-containing protein
F: Ntox15 domain-containing protein
G: Ntox15 domain-containing protein
H: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,86624
Polymers183,3638
Non-polymers1,50316
Water37821
1
A: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2715
Polymers22,9201
Non-polymers3504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1123
Polymers22,9201
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0162
Polymers22,9201
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2094
Polymers22,9201
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0162
Polymers22,9201
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0162
Polymers22,9201
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0162
Polymers22,9201
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ntox15 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2094
Polymers22,9201
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.472, 149.934, 176.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ntox15 domain-containing protein


Mass: 22920.369 Da / Num. of mol.: 8 / Mutation: H279A, D282A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides (bacteria) / Strain: MSK.16.10 / Plasmid: pET-DUET1 / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 2 M ammonium sulfate, 200 mM sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→48.64 Å / Num. obs: 51580 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.9
Reflection shellResolution: 2.9→3.24 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / Num. unique obs: 14277 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.64 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 2000 3.88 %
Rwork0.2018 --
obs0.204 51580 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11823 0 49 21 11893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612039
X-RAY DIFFRACTIONf_angle_d0.78916153
X-RAY DIFFRACTIONf_dihedral_angle_d5.361544
X-RAY DIFFRACTIONf_chiral_restr0.0451733
X-RAY DIFFRACTIONf_plane_restr0.0052090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.42371410.32513499X-RAY DIFFRACTION100
2.97-3.050.3521410.28643473X-RAY DIFFRACTION100
3.05-3.140.33591400.26373486X-RAY DIFFRACTION100
3.14-3.240.33491410.26763496X-RAY DIFFRACTION100
3.24-3.360.36831410.23813516X-RAY DIFFRACTION100
3.36-3.490.34681410.21873489X-RAY DIFFRACTION100
3.49-3.650.30241430.20893534X-RAY DIFFRACTION100
3.65-3.850.24161420.18933518X-RAY DIFFRACTION100
3.85-4.090.26991430.18143537X-RAY DIFFRACTION100
4.09-4.40.24591420.17043530X-RAY DIFFRACTION100
4.4-4.840.22171440.16233570X-RAY DIFFRACTION100
4.85-5.540.21461430.18763560X-RAY DIFFRACTION100
5.55-6.980.22071460.20163611X-RAY DIFFRACTION100
6.98-48.640.18831520.18213761X-RAY DIFFRACTION99

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