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- PDB-3o6q: The Structure of SpoIISA and SpoIISB, a Toxin - Antitoxin System -

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Basic information

Entry
Database: PDB / ID: 3o6q
TitleThe Structure of SpoIISA and SpoIISB, a Toxin - Antitoxin System
Components
  • Stage II sporulation protein SA
  • Stage II sporulation protein SB
KeywordsTOXIN/ANTITOXIN / GAF domain / toxin-antitoxin / sporulation / TOXIN - ANTITOXIN complex / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / : / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2720 / Antitoxin SpoIISB / Toxin SpoIISA, type II toxin-antitoxin system / Toxin SpoIISA, type II toxin-antitoxin system / Antitoxin SpoIISB, type II toxin-antitoxin system / Single helix bin / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle ...Alpha-Beta Plaits - #2720 / Antitoxin SpoIISB / Toxin SpoIISA, type II toxin-antitoxin system / Toxin SpoIISA, type II toxin-antitoxin system / Antitoxin SpoIISB, type II toxin-antitoxin system / Single helix bin / Single helix bin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Stage II sporulation protein SB / Stage II sporulation protein SA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLevdikov, V.M. / Blagova, E.V. / Lebedev, A.A. / Wilkinson, A.J. / Florek, P. / Barak, I.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The structure and interactions of SpoIISA and SpoIISB, a toxin-antitoxin system in Bacillus subtilis.
Authors: Florek, P. / Levdikov, V.M. / Blagova, E. / Lebedev, A.A. / Skrabana, R. / Resetarova, S. / Pavelcikova, P. / Barak, I. / Wilkinson, A.J.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stage II sporulation protein SA
B: Stage II sporulation protein SB
C: Stage II sporulation protein SA
D: Stage II sporulation protein SB


Theoretical massNumber of molelcules
Total (without water)50,4474
Polymers50,4474
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-78 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.028, 59.465, 112.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS ensembles :
ID
1
2

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Components

#1: Protein Stage II sporulation protein SA / Killer protein spoIISA


Mass: 18506.041 Da / Num. of mol.: 2 / Fragment: unp residues 92-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU12830, spoIISA, ykaC / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34853
#2: Protein Stage II sporulation protein SB / Antidote protein spoIISB


Mass: 6717.663 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU12820, spoIISB / Plasmid: pET-DUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34800
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.79 Å3/Da / Density % sol: 31.24 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: 21 % PEG 1500, 0.4 M MES, 0.2 M malic acid, 0.43 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97890, 0.97900, 0.97630
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2008
RadiationMonochromator: high resolution Si(311) cut and a lower resolution Si(111) cut
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.9791
30.97631
ReflectionResolution: 2.25→50 Å / Num. obs: 16022 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 56 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 18.9
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.7 / Num. unique all: 388 / % possible all: 44.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0081refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→48.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 23.834 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25778 650 5 %RANDOM
Rwork0.19589 ---
obs0.19884 12265 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.135 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-0 Å2
2--1.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 18 3122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223185
X-RAY DIFFRACTIONr_bond_other_d0.0040.022151
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9774319
X-RAY DIFFRACTIONr_angle_other_deg1.2013.0025258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5245376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2824.258155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62615583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4371518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023452
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02634
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 55 -
Rwork0.258 825 -
obs--92.73 %
Refinement TLS params.Method: refined / Origin x: -12.009 Å / Origin y: -3.77 Å / Origin z: 26.998 Å
111213212223313233
T0.2139 Å20.0205 Å2-0.0262 Å2-0.0918 Å2-0.0146 Å2--0.2244 Å2
L3.6786 °21.0439 °2-1.0798 °2-2.321 °2-0.3631 °2--2.1839 °2
S-0.1112 Å °0.0997 Å °-0.0795 Å °0.0129 Å °0.0422 Å °-0.1332 Å °0.1143 Å °-0.1806 Å °0.0691 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A97 - 241
2X-RAY DIFFRACTION1B9 - 51
3X-RAY DIFFRACTION1C98 - 241
4X-RAY DIFFRACTION1D9 - 52

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