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- PDB-4pu4: Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and ... -

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Basic information

Entry
Database: PDB / ID: 4pu4
TitleShewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex (space group P21)
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 / 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 / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix 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 / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / 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: 3.786 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-73 kcal/mol
Surface area52690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.240, 57.330, 171.380
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA0
211chain BB0
112chain CC0
212chain DD0

NCS ensembles :
ID
1
2

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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) / 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)
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.76 %
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)
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)11
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: 3.786→47.573 Å / Num. obs: 13858 / % possible obs: 97.03 % / Observed criterion σ(I): 1.21
Reflection shellHighest resolution: 3.786 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: 3.786→47.573 Å / SU ML: 0.57 / σ(F): 1.99 / Phase error: 33.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3064 693 5 %
Rwork0.2364 --
obs0.2399 13855 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.786→47.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7760 1003 0 0 8763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059037
X-RAY DIFFRACTIONf_angle_d0.94612444
X-RAY DIFFRACTIONf_dihedral_angle_d16.8043418
X-RAY DIFFRACTIONf_chiral_restr0.0351411
X-RAY DIFFRACTIONf_plane_restr0.0051431
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3550X-RAY DIFFRACTION10.694TORSIONAL
12B3550X-RAY DIFFRACTION10.694TORSIONAL
21C554X-RAY DIFFRACTION10.694TORSIONAL
22D554X-RAY DIFFRACTION10.694TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.786-4.07860.35871290.26982460X-RAY DIFFRACTION92
4.0786-4.48870.3451390.23262628X-RAY DIFFRACTION99
4.4887-5.13760.30211400.21962671X-RAY DIFFRACTION99
5.1376-6.47030.31391410.26822677X-RAY DIFFRACTION98
6.4703-47.57690.26991440.21772726X-RAY DIFFRACTION98

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