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- PDB-6ifm: Crystal structure of DNA bound VapBC from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 6ifm
TitleCrystal structure of DNA bound VapBC from Salmonella typhimurium
Components
  • Antitoxin VapB
  • DNA backward (27-MER)
  • DNA forward (27-MER)
  • tRNA(fMet)-specific endonuclease VapC
KeywordsTOXIN/ANTITOXIN/DNA / Toxin-Antitoxin / TOXIN-ANTITOXIN-DNA complex
Function / homology
Function and homology information


RNA nuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
: / : / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / : / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family ...: / : / Pemi-like Protein 1; Chain: D / Pemi-like Protein 1; Chain: D - #10 / : / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Ribbon / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin VapB / tRNA(fMet)-specific endonuclease VapC
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.804 Å
AuthorsPark, D.W. / Lee, B.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2018R1A2A1A19018526 Korea, Republic Of
National Research Foundation (Korea)2018R1A5A2024425 Korea, Republic Of
CitationJournal: Faseb J. / Year: 2020
Title: Crystal structure of proteolyzed VapBC and DNA-bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca2+-dependent ribonuclease.
Authors: Park, D. / Yoon, H.J. / Lee, K.Y. / Park, S.J. / Cheon, S.H. / Lee, H.H. / Lee, S.J. / Lee, B.J.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: tRNA(fMet)-specific endonuclease VapC
E: tRNA(fMet)-specific endonuclease VapC
C: tRNA(fMet)-specific endonuclease VapC
G: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin VapB
F: Antitoxin VapB
H: Antitoxin VapB
D: Antitoxin VapB
M: DNA forward (27-MER)
N: DNA backward (27-MER)


Theoretical massNumber of molelcules
Total (without water)107,12810
Polymers107,12810
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33370 Å2
ΔGint-147 kcal/mol
Surface area38230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.677, 93.677, 122.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
tRNA(fMet)-specific endonuclease VapC / RNase VapC / Toxin VapC


Mass: 14957.292 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: vapC, STM3033 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZM86, Hydrolases; Acting on ester bonds
#2: Protein
Antitoxin VapB


Mass: 7677.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: vapB, STM3034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CPV2
#3: DNA chain DNA forward (27-MER)


Mass: 8176.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA backward (27-MER)


Mass: 8412.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium citrate tribasic pH7, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 29329 / % possible obs: 99 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3
Reflection shellResolution: 2.8→2.886 Å / Rmerge(I) obs: 0.53 / Num. unique obs: 9280 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.804→48.867 Å / Cross valid method: THROUGHOUT / σ(F): 24.59 / Phase error: 23.28
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2331 1469 5.01 %
Rwork0.2063 --
obs0.2105 29329 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.804→48.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 1107 0 149 7596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087703
X-RAY DIFFRACTIONf_angle_d1.08910642
X-RAY DIFFRACTIONf_dihedral_angle_d15.3734445
X-RAY DIFFRACTIONf_chiral_restr0.0531200
X-RAY DIFFRACTIONf_plane_restr0.0071181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.805-2.90530.27821440.20172723X-RAY DIFFRACTION93
2.9053-3.02160.22441480.19432818X-RAY DIFFRACTION95
3.0216-3.15910.23531450.21862759X-RAY DIFFRACTION95
3.1591-3.32560.2651480.21692802X-RAY DIFFRACTION95
3.3256-3.53390.27061450.23042758X-RAY DIFFRACTION95
3.5339-3.80660.26751480.21962806X-RAY DIFFRACTION95
3.8066-4.18950.23891480.21852813X-RAY DIFFRACTION95
4.1895-4.79530.21141470.1922792X-RAY DIFFRACTION95
4.7953-6.03980.20471460.21162777X-RAY DIFFRACTION95
6.0398-48.87480.21741480.1972807X-RAY DIFFRACTION95

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