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- PDB-8pu4: FaRel2 bound to the ATP analogue, APCPP -

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Basic information

Entry
Database: PDB / ID: 8pu4
TitleFaRel2 bound to the ATP analogue, APCPP
ComponentsRelA/SpoT domain-containing protein
KeywordsANTITOXIN / Toxin / toxSAS / RSH / small alormone synthetase / phage defence
Function / homologyguanosine tetraphosphate biosynthetic process / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Nucleotidyltransferase superfamily / metal ion binding / : / RelA/SpoT domain-containing protein
Function and homology information
Biological speciesCoprobacillus sp. D7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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: FaRel2 bound to the ATP analogue, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,7679
Polymers74,1783
Non-polymers1,5896
Water1,78399
1
A: RelA/SpoT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2563
Polymers24,7261
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RelA/SpoT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2563
Polymers24,7261
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RelA/SpoT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2563
Polymers24,7261
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.498, 60.581, 177.157
Angle α, β, γ (deg.)90.000, 90.589, 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 RelA/SpoT domain-containing protein


Mass: 24726.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprobacillus sp. D7 (bacteria) / Gene: DXB93_19735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E3DY42
#2: Chemical ChemComp-DOU / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid


Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12 % w/v PEG 2000, 50 mM MES pH 5.5

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→59.1 Å / Num. obs: 16326 / % possible obs: 90.9 % / Redundancy: 13.5 % / Biso Wilson estimate: 51.19 Å2 / CC1/2: 0.985 / Net I/σ(I): 7.3
Reflection shellResolution: 2.62→2.83 Å / Num. unique obs: 818 / CC1/2: 0.332

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Processing

Software
NameVersionClassification
BUSTER1.19.2_4158refinement
autoPROC1.19.2_4158data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→59.05 Å / SU ML: 0.3659 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 755 4.62 %
Rwork0.1944 15571 -
obs0.1972 16326 80.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.56 Å2
Refinement stepCycle: LAST / Resolution: 2.62→59.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 96 99 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00964227
X-RAY DIFFRACTIONf_angle_d1.16985721
X-RAY DIFFRACTIONf_chiral_restr0.0655599
X-RAY DIFFRACTIONf_plane_restr0.0077711
X-RAY DIFFRACTIONf_dihedral_angle_d20.43891552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.820.3724270.2844749X-RAY DIFFRACTION19.5
2.82-3.110.34261670.2793165X-RAY DIFFRACTION82.27
3.11-3.560.26791860.22193843X-RAY DIFFRACTION100
3.56-4.480.24531950.16363863X-RAY DIFFRACTION99.95
4.48-59.050.22471800.17853951X-RAY DIFFRACTION99.9

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