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- PDB-4pu5: Shewanella oneidensis Toxin Antitoxin System Toxin Protein HipA B... -

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Basic information

Entry
Database: PDB / ID: 4pu5
TitleShewanella oneidensis Toxin Antitoxin System Toxin Protein HipA Bound with AMPPNP and Mg
ComponentsToxin-antitoxin system toxin HipA family
KeywordsTOXIN / Toxin Antitoxin System
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
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Serine/threonine-protein kinase toxin HipA
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.834 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 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Toxin-antitoxin system toxin HipA family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5345
Polymers50,9561
Non-polymers5784
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.700, 75.830, 110.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 50956.219 Da / Num. of mol.: 1
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M sodium chloride, 0.1 M HEPES sodium, pH 7.0, 25% PEG4000, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→44.61 Å / Num. obs: 45100 / Observed criterion σ(I): 3.17
Reflection shellHighest resolution: 1.83 Å

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1287) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DNV

3dnv


Resolution: 1.834→44.607 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 15.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1754 2255 5 %
Rwork0.1558 --
obs0.1568 45086 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.834→44.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 34 486 3986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053578
X-RAY DIFFRACTIONf_angle_d0.9484855
X-RAY DIFFRACTIONf_dihedral_angle_d13.4591322
X-RAY DIFFRACTIONf_chiral_restr0.052537
X-RAY DIFFRACTIONf_plane_restr0.003626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.834-1.87390.29161270.26552427X-RAY DIFFRACTION92
1.8739-1.91750.26451400.23032651X-RAY DIFFRACTION100
1.9175-1.96540.20251400.21092654X-RAY DIFFRACTION100
1.9654-2.01860.2341400.18252656X-RAY DIFFRACTION100
2.0186-2.0780.18591400.16332658X-RAY DIFFRACTION100
2.078-2.1450.18361380.15962635X-RAY DIFFRACTION100
2.145-2.22170.17951410.14992663X-RAY DIFFRACTION100
2.2217-2.31060.17441420.15662696X-RAY DIFFRACTION100
2.3106-2.41580.14761390.14232652X-RAY DIFFRACTION100
2.4158-2.54310.15811410.14452685X-RAY DIFFRACTION100
2.5431-2.70250.15491410.14282672X-RAY DIFFRACTION100
2.7025-2.91110.16781420.14842705X-RAY DIFFRACTION100
2.9111-3.2040.17931430.14992709X-RAY DIFFRACTION100
3.204-3.66740.18181430.1452715X-RAY DIFFRACTION100
3.6674-4.61980.14581460.12832773X-RAY DIFFRACTION100
4.6198-44.620.17211520.17112880X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 54.7179 Å / Origin y: 37.4797 Å / Origin z: 45.2995 Å
111213212223313233
T0.0722 Å2-0.0133 Å20.0093 Å2-0.0634 Å20.0064 Å2--0.1158 Å2
L0.8706 °20.0624 °2-0.0677 °2-0.8746 °20.2707 °2--2.8194 °2
S0.0389 Å °0.0226 Å °-0.0389 Å °-0.0875 Å °-0.0237 Å °-0.034 Å °0.1028 Å °-0.0976 Å °0.0019 Å °
Refinement TLS groupSelection details: all

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