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- PDB-8pu2: Structure of the antitoxin ATfaRel2 -

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Basic information

Entry
Database: PDB / ID: 8pu2
TitleStructure of the antitoxin ATfaRel2
ComponentsAntitoxin ATfaRel2, antidote of FaRel2
KeywordsANTITOXIN / Toxin / toxSAS / RSH / small alormone synthetase / phage defence
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesCoprobacillus sp. D7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.24 Å
AuthorsGarcia-Pino, A. / Talavera Perez, A. / Dominguez Molina, L.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)PDR T.0090.22 Belgium
CitationJournal: To Be Published
Title: Structure of the antitoxin ATfaRel2
Authors: Garcia-Pino, A. / Talavera Perez, A. / Dominguez Molina, L.
History
DepositionJul 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin ATfaRel2, antidote of FaRel2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5972
Polymers8,5021
Non-polymers951
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.289, 34.161, 37.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-241-

HOH

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Components

#1: Protein Antitoxin ATfaRel2, antidote of FaRel2


Mass: 8501.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprobacillus sp. D7 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % PEG 2000 MME pH 6.9

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.24→30.52 Å / Num. obs: 15179 / % possible obs: 92.6 % / Redundancy: 12.6 % / CC1/2: 0.998 / Net I/σ(I): 13
Reflection shellResolution: 1.24→1.37 Å / Num. unique obs: 759 / CC1/2: 0.711 / % possible all: 46.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
autoPROCdata processing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.24→30.52 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2084 772 5.09 %
Rwork0.1869 --
obs0.1881 15179 75.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→30.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 5 111 704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006613
X-RAY DIFFRACTIONf_angle_d0.881827
X-RAY DIFFRACTIONf_dihedral_angle_d12.741231
X-RAY DIFFRACTIONf_chiral_restr0.09189
X-RAY DIFFRACTIONf_plane_restr0.007105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.320.1673120.2793256X-RAY DIFFRACTION8
1.32-1.420.2843690.26791455X-RAY DIFFRACTION46
1.42-1.560.23091750.22593017X-RAY DIFFRACTION97
1.56-1.790.23661510.20853176X-RAY DIFFRACTION100
1.79-2.250.21481640.18933186X-RAY DIFFRACTION100
2.25-30.520.19742010.17293317X-RAY DIFFRACTION100

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