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- PDB-8pu1: Structure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP -

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Basic information

Entry
Database: PDB / ID: 8pu1
TitleStructure of the toxin/antitoxin complex FaRel/ATfaRel2 with APCPP
Components
  • ATfaRel2
  • RelA/SpoT domain-containing protein
KeywordsANTITOXIN / Toxin / toxSAS / RSH / small alormone synthetase
Function / homology
Function and homology information


guanosine tetraphosphate biosynthetic process / metal ion binding
Similarity search - Function
Protein of unknown function DUF6718 / Family of unknown function (DUF6718) / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / CACODYLATE ION / N-PROPANOL / RelA/SpoT domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesThomasclavelia ramosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 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 toxin/antitoxin complex FaRel/ATfaRel2 with APCPP
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
Revision 1.1Sep 25, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATfaRel2
B: RelA/SpoT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,84918
Polymers33,3772
Non-polymers1,47216
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)227.810, 227.810, 227.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11B-540-

HOH

21B-564-

HOH

31B-613-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ATfaRel2


Mass: 8501.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thomasclavelia ramosa (bacteria) / Gene: DXB93_19740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E3DY87
#2: Protein RelA/SpoT domain-containing protein


Mass: 24875.225 Da / Num. of mol.: 1 / Mutation: Y128F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thomasclavelia ramosa (bacteria) / Gene: DXB93_19735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E3DY42

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Non-polymers , 6 types, 351 molecules

#3: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.7 Å3/Da / Density % sol: 66.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3% v/v 2-Propanol and 0.1 M Sodium, pH 6.5

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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 9M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.7→52.26 Å / Num. obs: 55679 / % possible obs: 99.95 % / Redundancy: 68.4 % / Biso Wilson estimate: 40.61 Å2 / CC1/2: 1 / Net I/σ(I): 24.47
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 78533 / CC1/2: 0.399 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (24-FEB-2021)refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→52.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.091
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 2784 5 %RANDOM
Rwork0.2242 ---
obs0.2253 55679 99.9 %-
Displacement parametersBiso mean: 43.36 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.702→52.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 89 337 2664
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082369HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.863178HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d833SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes394HARMONIC5
X-RAY DIFFRACTIONt_it2369HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion16.37
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2490SEMIHARMONIC4
LS refinement shellResolution: 1.702→1.71 Å
RfactorNum. reflection% reflection
Rfree0.6297 -4.94 %
Rwork0.6486 1059 -
obs--97.1 %
Refinement TLS params.Method: refined / Origin x: -51.2751 Å / Origin y: -12.968 Å / Origin z: -42.2611 Å
111213212223313233
T0.0144 Å20.0076 Å20.0199 Å2--0.0107 Å2-0.0088 Å2---0.0258 Å2
L0.5633 °2-0.3118 °20.0025 °2-0.1741 °2-0.1115 °2--0.6728 °2
S-0.0153 Å °-0.0714 Å °0.0294 Å °0.0004 Å °0.037 Å °-0.0328 Å °-0.0729 Å °0.0264 Å °-0.0217 Å °
Refinement TLS groupSelection details: { *|* }

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