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- PDB-4ato: New insights into the mechanism of bacterial Type III toxin-antit... -

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Basic information

Entry
Database: PDB / ID: 4ato
TitleNew insights into the mechanism of bacterial Type III toxin-antitoxin systems: selective toxin inhibition by a non-coding RNA pseudoknot
Components
  • TOXI
  • TOXN
KeywordsTOXIN/ANTITOXIN / TOXIN-ANTITOXIN COMPLEX
Function / homology
Function and homology information


plasmid maintenance / RNA endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
ToxN/AbiQ toxin / Toxin ToxN, type III toxin-antitoxin system / Thiol Ester Dehydrase; Chain A - #130 / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Endoribonuclease ToxN
Similarity search - Component
Biological speciesBACILLUS THURINGIENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShort, F.L. / Pei, X.Y. / Blower, T.R. / Ong, S.L. / Luisi, B.F. / Salmond, G.P.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Selectivity and Self-Assembly in the Control of a Bacterial Toxin by an Antitoxic Noncoding RNA Pseudoknot.
Authors: Short, F.L. / Pei, X.Y. / Blower, T.R. / Ong, S.L. / Fineran, P.C. / Luisi, B.F. / Salmond, G.P.C.
History
DepositionMay 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOXN
G: TOXI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0343
Polymers33,9162
Non-polymers1181
Water3,999222
1
A: TOXN
G: TOXI
hetero molecules

A: TOXN
G: TOXI
hetero molecules

A: TOXN
G: TOXI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1029
Polymers101,7476
Non-polymers3553
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area15600 Å2
ΔGint-79.1 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.100, 127.100, 37.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein TOXN


Mass: 22928.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Strain: KURSTAKI HD-73 / Description: ENVIRONMENT ISOLATED FROM SCOTLAND SOIL, U.K / Plasmid: PFLS67 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q3YN09
#2: RNA chain TOXI


Mass: 10987.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THURINGIENSIS (bacteria) / Strain: KURSTAKI HD-73 / Description: ENVIRONMENT ISOLATED FROM SCOTLAND SOIL, U.K / Plasmid: PFLS44 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.68 Å3/Da / Density % sol: 59.1 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.4
Details: PRECIPITANT CONTAINS 0.2 M AMMONIUM PHOSPHATE, 0.1 M TRIS-HCL PH 8.5, 50% MPD. CRYSTALLIZATION WITH A SITTING DROP, VAPOUR DIFFUSION METHOD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.11→28 Å / Num. obs: 34618 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 11 % / Biso Wilson estimate: 40.36 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.6
Reflection shellResolution: 2.11→2.23 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XDB

2xdb


Resolution: 2.2→27.95 Å / SU ML: 0.71 / σ(F): 1.42 / Phase error: 20.38 / Stereochemistry target values: ML / Details: RESIDUES 1-4 AND 173-194 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.1917 1713 4.9 %
Rwork0.1602 --
obs0.1618 34618 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.841 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 46.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.0311 Å20 Å20 Å2
2--1.0311 Å20 Å2
3----2.0622 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 726 8 222 2338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062245
X-RAY DIFFRACTIONf_angle_d1.0833200
X-RAY DIFFRACTIONf_dihedral_angle_d15.693963
X-RAY DIFFRACTIONf_chiral_restr0.082377
X-RAY DIFFRACTIONf_plane_restr0.005287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.26470.28991490.2422731X-RAY DIFFRACTION100
2.2647-2.33780.28631160.22732794X-RAY DIFFRACTION100
2.3378-2.42130.23431370.21422715X-RAY DIFFRACTION100
2.4213-2.51820.24511290.21112776X-RAY DIFFRACTION100
2.5182-2.63270.30491680.21942707X-RAY DIFFRACTION100
2.6327-2.77140.25771610.20062731X-RAY DIFFRACTION100
2.7714-2.94490.20751320.16932775X-RAY DIFFRACTION100
2.9449-3.17190.1731270.14912737X-RAY DIFFRACTION100
3.1719-3.49060.17831360.14952751X-RAY DIFFRACTION100
3.4906-3.99440.17971500.13732735X-RAY DIFFRACTION100
3.9944-5.02780.13841520.11542713X-RAY DIFFRACTION100
5.0278-27.95270.17561560.16152740X-RAY DIFFRACTION100

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