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- PDB-7csy: Pseudomonas aeruginosa antitoxin HigA with higBA promoter -

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Basic information

Entry
Database: PDB / ID: 7csy
TitlePseudomonas aeruginosa antitoxin HigA with higBA promoter
Components
  • DNA (28-MER)
  • DNA (29-MER)
  • HTH cro/C1-type domain-containing protein
KeywordsANTITOXIN/DNA / dimer / ANTITOXIN-DNA COMPLEX
Function / homology
Function and homology information


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
THYMIDINE-5'-PHOSPHATE / 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: 2.29 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 1.1Apr 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 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0May 29, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH cro/C1-type domain-containing protein
B: HTH cro/C1-type domain-containing protein
C: HTH cro/C1-type domain-containing protein
D: HTH cro/C1-type domain-containing protein
E: DNA (28-MER)
F: DNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8577
Polymers62,5346
Non-polymers3221
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-115 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.255, 100.433, 68.795
Angle α, β, γ (deg.)90.000, 114.214, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 11259.780 Da / Num. of mol.: 4
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 DNA (28-MER)


Mass: 8667.626 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 DNA (29-MER)


Mass: 8827.723 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: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 0.1M HEPES pH7.5, 0.1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→29.66 Å / Num. obs: 71719 / % possible obs: 98.78 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.15 Å2 / CC1/2: 0.596 / Net I/σ(I): 33.8
Reflection shellResolution: 2.29→2.368 Å / Num. unique obs: 3415 / CC1/2: 0.401

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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: 2.29→29.66 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 29.7627 / Stereochemistry target values: GeoStd + Monomer Library
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2467 3870 5.4 %
Rwork0.2092 67849 -
obs0.2113 71719 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.44 Å2
Refinement stepCycle: LAST / Resolution: 2.29→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 1167 20 57 4216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864360
X-RAY DIFFRACTIONf_angle_d1.05456145
X-RAY DIFFRACTIONf_chiral_restr0.0541681
X-RAY DIFFRACTIONf_plane_restr0.0071600
X-RAY DIFFRACTIONf_dihedral_angle_d19.04112424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.310.39421070.36081871X-RAY DIFFRACTION75.5
2.31-2.340.33981340.34452428X-RAY DIFFRACTION96.39
2.34-2.370.36481380.3062401X-RAY DIFFRACTION97.13
2.37-2.410.33111410.30462393X-RAY DIFFRACTION96.9
2.41-2.440.34771370.31182399X-RAY DIFFRACTION95.99
2.44-2.480.40251410.31552409X-RAY DIFFRACTION97.44
2.48-2.520.33831360.30232380X-RAY DIFFRACTION96.81
2.52-2.560.34971400.28142435X-RAY DIFFRACTION98.13
2.56-2.60.31861410.27162466X-RAY DIFFRACTION97.68
2.6-2.650.30991400.26712456X-RAY DIFFRACTION97.63
2.65-2.70.28571400.2592444X-RAY DIFFRACTION97.92
2.7-2.750.35931360.26832376X-RAY DIFFRACTION97.9
2.75-2.810.35711370.26212427X-RAY DIFFRACTION98.24
2.81-2.880.30471370.25542513X-RAY DIFFRACTION98.26
2.88-2.950.30931400.25522424X-RAY DIFFRACTION99
2.95-3.030.30711380.26052448X-RAY DIFFRACTION98.89
3.03-3.120.35751400.26352483X-RAY DIFFRACTION98.35
3.12-3.220.25051350.23092423X-RAY DIFFRACTION98.12
3.22-3.340.26441390.20242465X-RAY DIFFRACTION99.24
3.34-3.470.20231400.19222456X-RAY DIFFRACTION98.41
3.47-3.630.23171430.2052463X-RAY DIFFRACTION99.05
3.63-3.820.24341440.19792452X-RAY DIFFRACTION99.58
3.82-4.060.20451410.17612490X-RAY DIFFRACTION99.62
4.06-4.370.19071410.16082480X-RAY DIFFRACTION99.47
4.37-4.810.17961400.15862465X-RAY DIFFRACTION99.73
4.81-5.50.20541430.17172473X-RAY DIFFRACTION99.66
5.5-6.910.22751430.17422490X-RAY DIFFRACTION99.62
6.91-29.660.1651380.15192439X-RAY DIFFRACTION98.25

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