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- PDB-5czf: Crystal structure of the PaaA2-ParE2 antitoxin-toxin complex -

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Basic information

Entry
Database: PDB / ID: 5czf
TitleCrystal structure of the PaaA2-ParE2 antitoxin-toxin complex
Components
  • PaaA2
  • Plasmid stabilization protein ParE
KeywordsTOXIN / toxin-antitoxin
Function / homology
Function and homology information


molecular adaptor activity
Similarity search - Function
: / Stability determinant / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Plasmid stabilization protein ParE / : / Type II toxin-antitoxin system RelE/ParE family toxin / Stability determinant domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli O157 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.671 Å
AuthorsLoris, R. / Sterckx, Y.G.J.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A unique hetero-hexadecameric architecture displayed by the Escherichia coli O157 PaaA2-ParE2 antitoxin-toxin complex.
Authors: Sterckx, Y.G. / Jove, T. / Shkumatov, A.V. / Garcia-Pino, A. / Geerts, L. / De Kerpel, M. / Lah, J. / De Greve, H. / Van Melderen, L. / Loris, R.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: PaaA2
B: PaaA2
C: Plasmid stabilization protein ParE
D: Plasmid stabilization protein ParE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1056
Polymers37,9134
Non-polymers1922
Water1,76598
1
A: PaaA2
D: Plasmid stabilization protein ParE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0533
Polymers18,9562
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-26 kcal/mol
Surface area7320 Å2
MethodPISA
2
B: PaaA2
C: Plasmid stabilization protein ParE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0533
Polymers18,9562
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-27 kcal/mol
Surface area6950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.560, 91.560, 185.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PaaA2


Mass: 6243.075 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157 (bacteria) / Gene: SS52_2228 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6F6Q9, UniProt: Q8XAD5*PLUS
#2: Protein Plasmid stabilization protein ParE / Plasmid stabilization system protein


Mass: 12713.380 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157 (bacteria) / Gene: relE2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D7C2L1, UniProt: A0A0H3JHG3*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium acetate pH 5.0, 1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.671→48.78 Å / Num. obs: 13723 / % possible obs: 99.91 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 17.62
Reflection shellResolution: 2.671→2.767 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.231 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1333 / % possible all: 99.33

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CW7

5cw7


Resolution: 2.671→48.777 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 685 5 %
Rwork0.2009 --
obs0.2035 13712 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.671→48.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 10 98 2258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042214
X-RAY DIFFRACTIONf_angle_d0.6113031
X-RAY DIFFRACTIONf_dihedral_angle_d12.4431342
X-RAY DIFFRACTIONf_chiral_restr0.045340
X-RAY DIFFRACTIONf_plane_restr0.005393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6714-2.87760.36561330.30322531X-RAY DIFFRACTION100
2.8776-3.16720.37111330.23092539X-RAY DIFFRACTION100
3.1672-3.62540.2631350.20482559X-RAY DIFFRACTION100
3.6254-4.5670.19111380.16762612X-RAY DIFFRACTION100
4.567-48.78480.23591460.19142786X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.92490.24410.1780.56840.46950.1829-0.00290.2550.0923-0.2950.0867-0.33560.06220.14360.06320.19890.06270.00730.2851-0.10510.318340.5257-20.8269-9.3279
20.74341.10980.90081.5991.57152.214-0.0271-0.10040.1473-0.6611-0.37790.5659-0.5854-0.3249-0.13940.12070.0415-0.00030.3045-0.03060.316818.4575-20.8826-16.6778
37.3139-0.3186-3.59030.03380.22061.7185-0.14931.3585-0.69430.4476-0.1941-0.22450.5705-0.7723-0.03660.793-0.0945-0.03610.2808-0.07110.357818.3113-44.400510.5117
40.0264-0.0360.04040.02650.00040.01990.0858-0.0877-0.740.1205-0.15220.33490.5462-0.49410.00220.3683-0.0585-0.03270.2979-0.00850.409120.7113-38.465826.8588
50.3653-0.03940.28570.9517-0.72770.5759-0.0897-0.18710.31490.74480.1349-0.3937-0.02750.26360.01940.41660.0825-0.10810.2913-0.0070.282837.4442-35.170624.5116
60.2155-0.3163-0.08820.42270.37790.35490.2149-0.5457-0.06130.4282-0.48370.5188-0.06620.0187-0.09340.1670.0248-0.01930.37680.00160.370621.2997-26.251621.7347
70.5673-0.0303-0.17930.21190.290.51480.01-0.0104-1.0426-0.1686-0.44050.10410.56640.14910.05220.43030.11330.10840.3715-0.06560.387434.2314-41.165916.2488
82.8222-1.4143-0.19561.71120.54190.24810.0217-0.22170.62370.2202-0.101-0.5347-0.03140.0012-0.00320.3545-0.02990.06830.31880.02250.279834.4515-29.150314.8464
90.5951.19060.03514.00581.50691.299-0.46550.3980.6792-1.3786-0.03671.307-1.3209-0.3726-0.15250.5606-0.0429-0.12790.33850.03280.300716.9812-27.95259.1863
100.07930.17060.08380.13690.21440.0236-0.0541-0.3579-0.4655-0.4444-0.09690.196-0.33540.08520.00060.3657-0.0079-0.0480.46110.00320.341826.6145-32.11136.1689
110.70880.8776-0.07311.0327-0.02950.29420.2267-0.54280.17830.0896-0.04060.2536-0.21330.68720.03290.2501-0.0036-0.01820.26110.02840.254619.8063-31.312414.5058
120.14140.1761-0.03880.2144-0.07720.0499-0.1046-0.1580.2792-0.19950.3322-0.15960.3975-0.18520.00540.32010.03580.00890.3785-0.03710.311322.7813-35.147314.9208
130.2416-0.01280.02260.04170.03620.0135-0.718-0.15390.81720.140.0401-0.3056-0.4961-0.4892-0.010.48740.061-0.03270.2179-0.06040.429329.1607-44.14336.0968
140.14660.5921-0.17720.25680.07620.72670.10150.1551-0.1252-0.197-0.00180.10440.1441-0.35340.0010.248-0.03750.0220.2684-0.03750.344924.1404-23.4887-9.15
150.04340.2427-0.15120.1533-0.16240.24730.0309-0.0170.17580.453-0.2897-0.2041-0.2137-0.1082-0.00980.34460.068-0.00920.37730.02790.273634.4333-18.59824.7155
160.4313-0.29730.95460.47470.26220.8686-0.0161-0.10280.0516-0.1696-0.2170.03120.1347-0.0928-0.02050.17090.00440.02790.2134-0.01140.202932.9086-22.8404-3.6646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 60 )
3X-RAY DIFFRACTION3chain 'B' and (resid 20 through 34 )
4X-RAY DIFFRACTION4chain 'B' and (resid 35 through 41 )
5X-RAY DIFFRACTION5chain 'B' and (resid 42 through 59 )
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 7 )
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 25 )
8X-RAY DIFFRACTION8chain 'C' and (resid 26 through 44 )
9X-RAY DIFFRACTION9chain 'C' and (resid 45 through 59 )
10X-RAY DIFFRACTION10chain 'C' and (resid 60 through 67 )
11X-RAY DIFFRACTION11chain 'C' and (resid 68 through 77 )
12X-RAY DIFFRACTION12chain 'C' and (resid 78 through 86 )
13X-RAY DIFFRACTION13chain 'C' and (resid 87 through 92 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 44 )
15X-RAY DIFFRACTION15chain 'D' and (resid 45 through 59 )
16X-RAY DIFFRACTION16chain 'D' and (resid 60 through 92 )

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