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- PDB-7csw: Pseudomonas aeruginosa antitoxin HigA with pa2440 promoter -

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Basic information

Entry
Database: PDB / ID: 7csw
TitlePseudomonas aeruginosa antitoxin HigA with pa2440 promoter
Components
  • (pa2440) x 2
  • HTH cro/C1-type domain-containing protein
KeywordsANTITOXIN/DNA / dimer / ANTITOXIN-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSong, Y.J. / Luo, G.H. / Bao, R.
CitationJournal: Environ.Microbiol. / Year: 2021
Title: Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs.
Authors: Song, Y. / Luo, G. / Zhu, Y. / Li, T. / Li, C. / He, L. / Zhao, N. / Zhao, C. / Yang, J. / Huang, Q. / Mu, X. / Tang, X. / Kang, M. / Wu, S. / He, Y. / Bao, R.
History
DepositionAug 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 2.0Jan 27, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Experimental preparation / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair_step.i_label_seq_id_1 / _ndb_struct_na_base_pair_step.i_label_seq_id_2 / _ndb_struct_na_base_pair_step.j_label_seq_id_1 / _ndb_struct_na_base_pair_step.j_label_seq_id_2 / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 3.0Oct 13, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / database_2 / entity / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / struct_asym / struct_conn / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _cell.volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.ls_R_factor_R_free / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_CC_half / _reflns.percent_possible_obs / _reflns_shell.d_res_high / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _symmetry.space_group_name_Hall
Revision 3.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HTH cro/C1-type domain-containing protein
A: HTH cro/C1-type domain-containing protein
C: pa2440
D: pa2440


Theoretical massNumber of molelcules
Total (without water)40,9664
Polymers40,9664
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.498, 58.498, 66.795
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein HTH cro/C1-type domain-containing protein


Mass: 11259.780 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA4674 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HVC1
#2: DNA chain pa2440


Mass: 9171.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: DNA chain pa2440


Mass: 9275.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.61 Å3/Da / Density % sol: 23.63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 1M KCl, 0.1M Na-HEPES pH7.5, 1M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.969→40.36 Å / Num. obs: 18109 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 29.03 Å2 / Rmerge(I) obs: 0.169 / Net I/σ(I): 14.4
Reflection shellResolution: 1.97→2.04 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F8H

6f8h


Resolution: 1.97→40.36 Å / SU ML: 0.214 / Cross valid method: FREE R-VALUE / σ(F): 0.95 / Phase error: 23.656 / Stereochemistry target values: GEOSTD + MONOMER LIBRARY
RfactorNum. reflection% reflection
Rfree0.234 1819 10.04 %
Rwork0.197 --
obs0.201 18109 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1448 287 0 111 1846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081797
X-RAY DIFFRACTIONf_angle_d0.8922487
X-RAY DIFFRACTIONf_dihedral_angle_d16.4171031
X-RAY DIFFRACTIONf_chiral_restr0.062278
X-RAY DIFFRACTIONf_plane_restr0.004276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.25951380.22921302X-RAY DIFFRACTION100
2.02-2.080.28211340.21681242X-RAY DIFFRACTION100
2.08-2.150.2611460.20721244X-RAY DIFFRACTION100
2.15-2.230.32071300.20191235X-RAY DIFFRACTION100
2.23-2.310.2261450.1921262X-RAY DIFFRACTION100
2.31-2.420.26221380.20271255X-RAY DIFFRACTION100
2.42-2.550.28651400.21911267X-RAY DIFFRACTION100
2.55-2.710.28081400.21071246X-RAY DIFFRACTION100
2.71-2.920.22821400.22111244X-RAY DIFFRACTION100
2.92-3.210.29771480.23511240X-RAY DIFFRACTION99
3.21-3.670.22891330.19881269X-RAY DIFFRACTION100
3.67-4.630.19551470.16441226X-RAY DIFFRACTION100
4.63-40.360.17411400.17161258X-RAY DIFFRACTION100

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