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- PDB-24io: Crystal structure of the RelSeq N-terminal domain from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 24io
TitleCrystal structure of the RelSeq N-terminal domain from Streptococcus equisimilis in complex with pppGpp
ComponentsBifunctional (p)ppGpp synthase/hydrolase RelA
KeywordsTRANSFERASE / RelSeq / bifunctional enzyme / RelA/SpoT homolog / stringent response / Streptococcus equisimilis / alarmone / pppGpp
Function / homology
Function and homology information


guanosine-3',5'-bis(diphosphate) 3'-diphosphatase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity / GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / GTP binding / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT AH domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain ...RelA/SpoT, AH and RIS domains / RelA/SpoT AH domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / HD domain / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain profile. / ACT domain / HD domain profile. / ACT-like domain / HD domain / TGS-like / TGS domain profile. / TGS / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta-grasp domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-0O2 / : / Bifunctional (p)ppGpp synthase/hydrolase RelA
Similarity search - Component
Biological speciesStreptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKorban, S.A. / Kasatsky, P.S. / Spiridonova, Z.A. / Gurzhiy, V.V. / Paleskava, A.V. / Konevega, A.L. / Vinogradova, D.S.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Science Foundation23-74-10088 Russian Federation
St. Petersburg State University126022017738-9 Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of the RelSeq N-terminal domain from Streptococcus equisimilis in complex with pppGpp
Authors: Korban, S.A. / Kasatsky, P.S. / Spiridonova, Z.A. / Gurzhiy, V.V. / Paleskava, A.V. / Konevega, A.L. / Vinogradova, D.S.
History
DepositionMar 4, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional (p)ppGpp synthase/hydrolase RelA
B: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,78923
Polymers91,2132
Non-polymers3,57621
Water1,802100
1
A: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63417
Polymers45,6061
Non-polymers2,02716
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16560 Å2
MethodPISA
2
B: Bifunctional (p)ppGpp synthase/hydrolase RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1556
Polymers45,6061
Non-polymers1,5495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.751, 44.985, 126.433
Angle α, β, γ (deg.)90.000, 110.083, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional (p)ppGpp synthase/hydrolase RelA


Mass: 45606.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Gene: relA, rel / Production host: Escherichia coli (E. coli)
References: UniProt: Q54089, GTP diphosphokinase, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase

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Non-polymers , 5 types, 121 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-0O2 / guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)


Mass: 683.140 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18N5O20P5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, pH 8.5, 24% PEG8000, 1M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→118.7 Å / Num. obs: 14251 / % possible obs: 90.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 15.14 Å2 / CC1/2: 0.838 / Net I/σ(I): 4.2
Reflection shellResolution: 3.2→3.3 Å / Num. unique obs: 713 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProdata collection
autoPROC20250717data processing
STARANISOdata scaling
PHENIXphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→58.52 Å / SU ML: 0.4789 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2987 695 4.9 %
Rwork0.2419 13485 -
obs0.2447 14180 90.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.8 Å2
Refinement stepCycle: LAST / Resolution: 3.2→58.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 0 213 100 5492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525514
X-RAY DIFFRACTIONf_angle_d0.79497468
X-RAY DIFFRACTIONf_chiral_restr0.0408835
X-RAY DIFFRACTIONf_plane_restr0.0059916
X-RAY DIFFRACTIONf_dihedral_angle_d14.34782055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.440.3469980.27051982X-RAY DIFFRACTION67.16
3.44-3.790.2991310.25342793X-RAY DIFFRACTION94.87
3.79-4.340.35771610.24362866X-RAY DIFFRACTION97.8
4.34-5.470.26041590.2242913X-RAY DIFFRACTION98.18
5.47-58.520.24451460.22772931X-RAY DIFFRACTION94.82

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