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- PDB-7csv: Pseudomonas aeruginosa antitoxin HigA -

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Basic information

Entry
Database: PDB / ID: 7csv
TitlePseudomonas aeruginosa antitoxin HigA
ComponentsHTH cro/C1-type domain-containing protein
KeywordsANTITOXIN / dimer
Function / homologyToxin-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 / DNA binding / HTH cro/C1-type domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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

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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


Theoretical massNumber of molelcules
Total (without water)22,5202
Polymers22,5202
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-22 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.689, 65.689, 140.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

21B-262-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.94 Å3/Da / Density % sol: 36.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.707→19.54 Å / Num. obs: 33999 / % possible obs: 99.9 % / Redundancy: 33.8 % / Biso Wilson estimate: 15.87 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Net I/σ(I): 6.4
Reflection shellResolution: 1.707→1.768 Å / Num. unique obs: 1875 / CC1/2: 0.993

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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: 1.71→19.54 Å / SU ML: 0.195 / Cross valid method: FREE R-VALUE / σ(F): 1.68 / Phase error: 22.5474 / Stereochemistry target values: GeoStd + Monomer Library
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2226 3363 9.89 %
Rwork0.1789 30636 -
obs0.1833 33999 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.71→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 0 135 1667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631563
X-RAY DIFFRACTIONf_angle_d0.80852116
X-RAY DIFFRACTIONf_chiral_restr0.0638232
X-RAY DIFFRACTIONf_plane_restr0.0054280
X-RAY DIFFRACTIONf_dihedral_angle_d15.6284952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.730.29641490.28741367X-RAY DIFFRACTION97.12
1.73-1.760.25021470.22091320X-RAY DIFFRACTION97.35
1.76-1.780.25391510.22851322X-RAY DIFFRACTION96.15
1.78-1.810.31481420.2261355X-RAY DIFFRACTION96.64
1.81-1.850.27071410.20821342X-RAY DIFFRACTION95.68
1.85-1.880.32151360.19841313X-RAY DIFFRACTION96.73
1.88-1.920.26131350.1971322X-RAY DIFFRACTION95.42
1.92-1.950.28021550.18521316X-RAY DIFFRACTION95.21
1.95-20.25081410.18231329X-RAY DIFFRACTION95.39
2-2.040.22311390.18481308X-RAY DIFFRACTION94.89
2.04-2.090.21971420.18831283X-RAY DIFFRACTION93.87
2.09-2.150.20191470.17121308X-RAY DIFFRACTION93.75
2.15-2.210.20711490.16621289X-RAY DIFFRACTION93.56
2.21-2.290.23951410.17431261X-RAY DIFFRACTION92.6
2.29-2.370.18271400.181269X-RAY DIFFRACTION91.91
2.37-2.460.26551390.17561292X-RAY DIFFRACTION92.56
2.46-2.570.22791470.17371253X-RAY DIFFRACTION91.38
2.57-2.710.22751420.18921231X-RAY DIFFRACTION90.27
2.71-2.880.24031340.1881248X-RAY DIFFRACTION90.21
2.88-3.10.23691370.181245X-RAY DIFFRACTION89.62
3.1-3.410.21671260.17311230X-RAY DIFFRACTION88.45
3.41-3.90.17951410.15741194X-RAY DIFFRACTION87.6
3.9-4.90.17421310.14641180X-RAY DIFFRACTION85.41
4.9-19.540.19961110.17351059X-RAY DIFFRACTION75.83

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