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- PDB-7ycu: Heterotetramer of Antitoxin PrpA together with Toxin PrpT from Ps... -

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Basic information

Entry
Database: PDB / ID: 7ycu
TitleHeterotetramer of Antitoxin PrpA together with Toxin PrpT from Pseudoalteromonas rubra
Components
  • Antitoxin ParD
  • Toxin
KeywordsTOXIN/ANTITOXIN / ParE/RelE toxin / ParD antitoxin / RHH / DNA binding motif / Neutralization / ANTITOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Toxin-antitoxin system, toxin component ParE1/4 / Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH / Antitoxin ParD / Antitoxin ParD superfamily / : / ParE toxin of type II toxin-antitoxin system, parDE / Toxin-antitoxin system, RelE/ParE toxin family / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / Ribbon-helix-helix
Similarity search - Domain/homology
Toxin / Antitoxin ParD
Similarity search - Component
Biological speciesPseudoalteromonas rubra (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWang, C.C. / Niu, C.Y. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Front Microbiol / Year: 2022
Title: Structural insights into the PrpTA toxin-antitoxin system in Pseudoalteromonas rubra.
Authors: Wang, C. / Niu, C. / Hidayatullah, K.M. / Xue, L. / Zhu, Z. / Niu, L.
History
DepositionJul 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin
B: Antitoxin ParD
C: Toxin
D: Antitoxin ParD


Theoretical massNumber of molelcules
Total (without water)46,1944
Polymers46,1944
Non-polymers00
Water6,377354
1
A: Toxin
D: Antitoxin ParD

B: Antitoxin ParD
C: Toxin


Theoretical massNumber of molelcules
Total (without water)46,1944
Polymers46,1944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area11170 Å2
ΔGint-64 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.782, 83.085, 56.489
Angle α, β, γ (deg.)90.000, 91.660, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Toxin


Mass: 11412.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas rubra (bacteria) / Gene: AT705_24520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U2Y7P6
#2: Protein Antitoxin ParD


Mass: 11683.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas rubra (bacteria) / Gene: AT705_24525 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U3H4C4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Sodium cacodylate pH 6.0, 15 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.79→44.76 Å / Num. obs: 38264 / % possible obs: 98.64 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.43 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08416 / Rpim(I) all: 0.03478 / Rrim(I) all: 0.0912 / Net I/σ(I): 16.7
Reflection shellResolution: 1.79→1.857 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7912 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3740 / CC1/2: 0.809 / CC star: 0.946 / Rpim(I) all: 0.3588 / Rrim(I) all: 0.8715 / % possible all: 97.22

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→44.76 Å / SU ML: 0.1801 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2 1919 5.02 %
Rwork0.1675 36334 -
obs0.1691 38253 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.5 Å2
Refinement stepCycle: LAST / Resolution: 1.79→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 0 354 3242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962942
X-RAY DIFFRACTIONf_angle_d1.41443974
X-RAY DIFFRACTIONf_chiral_restr0.1022432
X-RAY DIFFRACTIONf_plane_restr0.0091526
X-RAY DIFFRACTIONf_dihedral_angle_d14.0571098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.28781490.23512508X-RAY DIFFRACTION97.18
1.84-1.890.24781480.21242579X-RAY DIFFRACTION97.64
1.89-1.940.23351160.19742571X-RAY DIFFRACTION97.82
1.94-2.010.25191170.18652587X-RAY DIFFRACTION98.36
2.01-2.080.2121280.16632586X-RAY DIFFRACTION98.37
2.08-2.160.2211310.15742579X-RAY DIFFRACTION98.47
2.16-2.260.19661530.1622595X-RAY DIFFRACTION98.88
2.26-2.380.22091520.1632581X-RAY DIFFRACTION98.91
2.38-2.530.23111400.16792588X-RAY DIFFRACTION99.09
2.53-2.720.21021420.18162611X-RAY DIFFRACTION99.31
2.72-30.1841480.17152606X-RAY DIFFRACTION98.96
3-3.430.20781150.16882641X-RAY DIFFRACTION99.49
3.43-4.320.18111350.14722645X-RAY DIFFRACTION99.64
4.32-44.760.16181450.162657X-RAY DIFFRACTION98.94

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