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- PDB-6n90: YoeB/ParE toxin from Agrobacterium tumefaciens -

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Basic information

Entry
Database: PDB / ID: 6n90
TitleYoeB/ParE toxin from Agrobacterium tumefaciens
ComponentsUncharacterized protein
KeywordsTOXIN
Function / homology
Function and homology information


RNA catabolic process / endonuclease activity
Similarity search - Function
Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
6-tungstotellurate(VI) / Putative mRNA interferase YoeB
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 Å
AuthorsBourne, C.R. / Reddem, E.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 United States
Citation
Journal: Front Microbiol / Year: 2020
Title: Identifying a Molecular Mechanism That Imparts Species-Specific Toxicity to YoeB Toxins.
Authors: Ames, J.R. / McGillick, J. / Murphy, T. / Reddem, E. / Bourne, C.R.
#1: Journal: Biorxiv / Year: 2019
Title: YoeB/ParE toxin from Agrobacterium tumefaciens
Authors: McGillick, J. / Ames, J.R. / Murphy, T. / Reddem, E. / Bourne, C.R.
History
DepositionNov 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3333
Polymers22,7182
Non-polymers1,6151
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Verified by MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.955, 77.739, 36.350
Angle α, β, γ (deg.)90.000, 92.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein


Mass: 11358.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: C58 / Gene: Atu2017 / Plasmid: pET28 / Details (production host): modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9CID9
#2: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 36.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 5% v/v 2-Methyl-2,4-pentanediol, 10% Polyethylene glycol 6000, 1 mM TEW

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→38.87 Å / Num. obs: 18587 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 9.4 / Num. measured all: 63456
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.733.30.69550.7210.3790.71292.3
1.75-1.813.20.0561400.990.0360.06798.8

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6Q

2a6q


Resolution: 1.755→38.87 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1685 10.06 %RANDOM
Rwork0.2183 15063 --
obs0.2213 16748 97.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.48 Å2 / Biso mean: 28.1072 Å2 / Biso min: 13.71 Å2
Refinement stepCycle: final / Resolution: 1.755→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 31 122 1583
Biso mean--29.67 28.29 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011520
X-RAY DIFFRACTIONf_angle_d1.1862125
X-RAY DIFFRACTIONf_chiral_restr0.052202
X-RAY DIFFRACTIONf_plane_restr0.005253
X-RAY DIFFRACTIONf_dihedral_angle_d15.068547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7551-1.80670.34071320.2651295142798
1.8067-1.8650.33191470.26641221136897
1.865-1.93170.30371500.26721227137796
1.9317-2.0090.30381370.25051266140399
2.009-2.10050.28251440.23281257140199
2.1005-2.21120.27951470.22611271141898
2.2112-2.34970.271360.23891250138698
2.3497-2.53110.26431330.22481264139798
2.5311-2.78580.2611450.231260140597
2.7858-3.18870.24811350.22091230136596
3.1887-4.01680.21410.20531264140598
4.0168-38.8790.21391380.18781258139695

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