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- PDB-6xrw: Chromosomal ParDE TA system from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6xrw
TitleChromosomal ParDE TA system from P. aeruginosa
Components
  • Plasmid stabilisation system protein
  • Ribbon-helix-helix protein, CopG family
KeywordsTOXIN/ANTITOXIN / toxin antitoxin system / ParE toxin ParD antitoxin type II TA system / TOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / STAT transcription factor, N-terminal domain superfamily / Toxin-antitoxin system, RelE/ParE toxin domain superfamily
Similarity search - Domain/homology
BENZAMIDINE / Ribbon-helix-helix protein, CopG family / Plasmid stabilisation system protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBourne, C.R. / Snead, K.J. / Thomas, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P20GM103640 United States
CitationJournal: Biochemistry / Year: 2022
Title: ParD Antitoxin Hotspot Alters a Disorder-to-Order Transition upon Binding to Its Cognate ParE Toxin, Lessening Its Interaction Affinity and Increasing Its Protease Degradation Kinetics.
Authors: Snead, K.J. / Moore, L.L. / Bourne, C.R.
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Plasmid stabilisation system protein
B: Ribbon-helix-helix protein, CopG family
C: Plasmid stabilisation system protein
D: Ribbon-helix-helix protein, CopG family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,67210
Polymers39,7694
Non-polymers9036
Water7,548419
1
A: Plasmid stabilisation system protein
B: Ribbon-helix-helix protein, CopG family
hetero molecules

A: Plasmid stabilisation system protein
B: Ribbon-helix-helix protein, CopG family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,20712
Polymers39,7694
Non-polymers1,4388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area10950 Å2
ΔGint-61 kcal/mol
Surface area17330 Å2
MethodPISA
2
C: Plasmid stabilisation system protein
D: Ribbon-helix-helix protein, CopG family
hetero molecules

C: Plasmid stabilisation system protein
D: Ribbon-helix-helix protein, CopG family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1388
Polymers39,7694
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area11170 Å2
ΔGint-53 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.401, 121.323, 58.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-117-

HOH

21D-225-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Plasmid stabilisation system protein / ParE toxin / Plasmid stabilization protein / Plasmid stabilization system protein / RelE/ParE ...ParE toxin / Plasmid stabilization protein / Plasmid stabilization system protein / RelE/ParE family toxin / Type II toxin-antitoxin system RelE/ParE family toxin


Mass: 10890.642 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ALP65_02189, C0044_00935, CAZ10_15820, CGU42_21595, DT376_01585, DZ962_27795, ECC04_014080, F3H14_16060, F6X67_25435, F7O92_13145, F8137_22785, FC629_00725, FDK04_00710, FEM29_10625, FZE40_ ...Gene: ALP65_02189, C0044_00935, CAZ10_15820, CGU42_21595, DT376_01585, DZ962_27795, ECC04_014080, F3H14_16060, F6X67_25435, F7O92_13145, F8137_22785, FC629_00725, FDK04_00710, FEM29_10625, FZE40_26955, FZE44_21675, FZE49_19155, GEZ68_19720, GNQ12_20765, GNQ27_19805, GNQ36_15570, GNQ40_21605, GNQ44_11770, GNQ48_08755, GNQ66_20720, GRH68_21070, GRH69_08580, IPC36_01505, IPC669_21920, NCTC10662_01006, NCTC11839_02383, NCTC13621_04834, PaeAG1_00136, RW109_RW109_00727
Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A072ZG36
#2: Protein Ribbon-helix-helix protein, CopG family / ParD antitoxin / Transcriptional regulator


Mass: 8994.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: DY930_22595, E4V10_10535, F7O96_16600, GNQ12_20760, IPC1509_05415, IPC584_11760, NCTC10299_03548, NCTC12934_01716, PAMH19_0124, PA0125
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069QCW3

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Non-polymers , 4 types, 425 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1:1 mixture of precipitant 7.5% MPD, 20% PEG 6000, 25 mM (NH4)2SO4, 100 mM Tris pH 7.0 with protein solution 10.5 mg/mL ParDE in 25 mM MES pH 6.0, 150 mM NaCl, 2.5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 25, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 33497 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.022 / Rrim(I) all: 0.054 / Χ2: 0.798 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.20.27615740.90.2160.3520.51895.3
1.83-1.862.60.27615820.9110.2060.3460.50198.2
1.86-1.92.80.26316310.9350.1870.3240.52699.3
1.9-1.9430.21916070.9470.1470.2650.59299.4
1.94-1.983.40.18616260.9680.1160.220.60499.9
1.98-2.033.80.1616260.9750.0920.1850.76299.9
2.03-2.084.20.14216420.9840.0760.1610.83399.9
2.08-2.134.70.12816270.9890.0640.1440.85299.8
2.13-2.25.20.10616260.9910.0510.1180.86299.8
2.2-2.2760.09916440.9950.0440.1090.82799.9
2.27-2.356.40.08216410.9970.0350.090.708100
2.35-2.446.60.07416540.9970.0310.080.689100
2.44-2.556.70.06416340.9980.0270.0690.665100
2.55-2.696.80.05716410.9990.0240.0620.71100
2.69-2.866.70.04916490.9990.0210.0530.709100
2.86-3.086.60.04416610.9990.0180.0480.724100
3.08-3.396.60.03616720.9990.0150.0390.777100
3.39-3.886.40.03416740.9990.0150.0371.042100
3.88-4.886.20.03517030.9990.0150.0381.232100
4.88-505.30.02817740.9990.0140.0311.06999.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZE

5cze


Resolution: 1.77→27.86 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 1999 5.97 %
Rwork0.1775 31498 -
obs0.1799 33497 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.28 Å2 / Biso mean: 24.1216 Å2 / Biso min: 5.95 Å2
Refinement stepCycle: final / Resolution: 1.77→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 61 419 3178
Biso mean--27.29 35.97 -
Num. residues----339
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.77-1.820.35581340.26682107224193
1.82-1.870.25031420.24212238238098
1.87-1.920.31051430.2092261240499
1.92-1.980.25051460.197822972443100
1.98-2.050.24631440.189622662410100
2.05-2.140.24591450.190322962441100
2.14-2.230.23091460.181922982444100
2.23-2.350.2191470.184523072454100
2.35-2.50.21381460.186922792425100
2.5-2.690.261450.186623062451100
2.69-2.960.22251460.18452293243999
2.96-3.390.20881120.16061758187076
3.39-4.270.15851490.14592341249099
4.27-27.860.20691540.162624512605100

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