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- PDB-6ifc: Crystal structure of VapBC from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 6ifc
TitleCrystal structure of VapBC from Salmonella typhimurium
Components
  • (Antitoxin VapB) x 2
  • tRNA(fMet)-specific endonuclease VapC
KeywordsTOXIN/ANTITOXIN / Toxin-Antitoxin / TOXIN-ANTITOXIN 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
SpoVT-AbrB domain profile. / SpoVT-AbrB domain / PIN domain / SpoVT-AbrB domain superfamily / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Antitoxin VapB / tRNA(fMet)-specific endonuclease VapC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPark, D.W. / Lee, B.J.
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 19, 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 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin VapB
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin VapB
E: tRNA(fMet)-specific endonuclease VapC
F: Antitoxin VapB
G: tRNA(fMet)-specific endonuclease VapC
H: Antitoxin VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,56012
Polymers71,3998
Non-polymers1604
Water3,711206
1
A: tRNA(fMet)-specific endonuclease VapC
B: Antitoxin VapB
C: tRNA(fMet)-specific endonuclease VapC
D: Antitoxin VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7806
Polymers35,7004
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-61 kcal/mol
Surface area13610 Å2
MethodPISA
2
E: tRNA(fMet)-specific endonuclease VapC
F: Antitoxin VapB
G: tRNA(fMet)-specific endonuclease VapC
H: Antitoxin VapB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7806
Polymers35,7004
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-63 kcal/mol
Surface area13400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.956, 114.942, 53.998
Angle α, β, γ (deg.)90.00, 114.12, 90.00
Int Tables number4
Space group name H-MP1211

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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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (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/peptide Antitoxin VapB


Mass: 2537.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: vapB, STM3034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CPV2
#3: Protein/peptide Antitoxin VapB


Mass: 3247.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: vapB, STM3034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CPV2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M CAPS/ Sodium hydroxide pH 10.5, 2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.99→57.47 Å / Num. obs: 38222 / % possible obs: 93.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.61
Reflection shellResolution: 2→2.03 Å / CC1/2: 0.942 / Rpim(I) all: 0.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TND

3tnd


Resolution: 1.99→57.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.751 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23833 1905 5 %RANDOM
Rwork0.17527 ---
obs0.17832 36229 93.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.647 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å2-0.17 Å2
2---0.98 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.99→57.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 4 206 5186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195070
X-RAY DIFFRACTIONr_bond_other_d0.0010.024824
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9516848
X-RAY DIFFRACTIONr_angle_other_deg0.837311082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91223.388242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61315892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3881548
X-RAY DIFFRACTIONr_chiral_restr0.0920.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0023.382504
X-RAY DIFFRACTIONr_mcbond_other2.9943.3792503
X-RAY DIFFRACTIONr_mcangle_it4.2575.0423116
X-RAY DIFFRACTIONr_mcangle_other4.2565.0443117
X-RAY DIFFRACTIONr_scbond_it3.9193.862566
X-RAY DIFFRACTIONr_scbond_other3.9183.8612567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0225.6163733
X-RAY DIFFRACTIONr_long_range_B_refined8.05727.5126018
X-RAY DIFFRACTIONr_long_range_B_other8.05627.4515976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 141 -
Rwork0.228 2581 -
obs--90.46 %

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