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- PDB-4pu3: Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and ... -

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Basic information

Entry
Database: PDB / ID: 4pu3
TitleShewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex (space group P212121)
Components
  • (Operator DNA) x 2
  • Toxin-antitoxin system antidote transcriptional repressor Xre family
  • Toxin-antitoxin system toxin HipA family
KeywordsTOXIN/ANTITOXIN/DNA / Toxin Antitoxin System / TOXIN-ANTITOXIN-DNA complex
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA binding / ATP binding / cytosol
Similarity search - Function
HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Serine/threonine-protein kinase toxin HipA / Antitoxin HipB
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsWen, Y. / Behiels, E. / Felix, J. / Elegheert, J. / Vergauwen, B. / Devreese, B. / Savvides, S.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence.
Authors: Wen, Y. / Behiels, E. / Felix, J. / Elegheert, J. / Vergauwen, B. / Devreese, B. / Savvides, S.N.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Sep 20, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin-antitoxin system toxin HipA family
B: Toxin-antitoxin system toxin HipA family
D: Toxin-antitoxin system antidote transcriptional repressor Xre family
Q: Operator DNA
C: Toxin-antitoxin system antidote transcriptional repressor Xre family
P: Operator DNA


Theoretical massNumber of molelcules
Total (without water)144,2086
Polymers144,2086
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11220 Å2
ΔGint-87 kcal/mol
Surface area50960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.820, 122.450, 189.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C and ( resid 19 through 86 )
22chain D and ( resid 19 through 86 )
13chain C and ( resid 95 through 97 )
23chain D and ( resid 95 through 97 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0
211chain BB0
112chain C and ( resid 19 through 86 )C0
212chain D and ( resid 19 through 86 )D0
113chain E and ( resid 95 through 97 )C0
213chain F and ( resid 95 through 97 )D0

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Toxin-antitoxin system toxin HipA family /


Mass: 51167.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_0706 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EIX3
#2: Protein Toxin-antitoxin system antidote transcriptional repressor Xre family / / HipB


Mass: 12951.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_0705 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EIX4
#3: DNA chain Operator DNA


Mass: 8036.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: strand 1 / Source: (synth.) Shewanella oneidensis (bacteria)
#4: DNA chain Operator DNA


Mass: 7933.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: strand 2 / Source: (synth.) Shewanella oneidensis (bacteria)

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.2 M calcium acetate hydrate, pH 7.5, 20% PEG3350, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1311
SYNCHROTRONSLS X06DA21
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELMar 12, 2013
DECTRIS PILATUS 2M-F2PIXELMay 5, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.39→49.39 Å / Num. all: 19211 / Num. obs: 19211 / % possible obs: 98.93 % / Observed criterion σ(I): 1.81
Reflection shellHighest resolution: 3.39 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: dev_1287)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DNV

3dnv


Resolution: 3.39→49.381 Å / SU ML: 0.57 / σ(F): 1.99 / Phase error: 35.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3154 960 5 %RANDOM
Rwork0.256 ---
obs0.259 19187 98.81 %-
all-19187 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.39→49.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7801 1004 0 0 8805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039083
X-RAY DIFFRACTIONf_angle_d0.812508
X-RAY DIFFRACTIONf_dihedral_angle_d15.6833425
X-RAY DIFFRACTIONf_chiral_restr0.0331410
X-RAY DIFFRACTIONf_plane_restr0.0041442
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3919X-RAY DIFFRACTION11.107TORSIONAL
12B3919X-RAY DIFFRACTION11.107TORSIONAL
21C633X-RAY DIFFRACTION11.107TORSIONAL
22D633X-RAY DIFFRACTION11.107TORSIONAL
31C18X-RAY DIFFRACTION11.107TORSIONAL
32D18X-RAY DIFFRACTION11.107TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.39-3.56890.39661280.32932433X-RAY DIFFRACTION95
3.5689-3.79240.37111350.29592560X-RAY DIFFRACTION99
3.7924-4.08510.30031360.25942591X-RAY DIFFRACTION99
4.0851-4.49590.31421380.2412602X-RAY DIFFRACTION100
4.4959-5.14590.30571360.22662611X-RAY DIFFRACTION100
5.1459-6.4810.31621410.26772671X-RAY DIFFRACTION100
6.481-49.38580.27971460.23482759X-RAY DIFFRACTION99

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