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- PDB-8acu: Structure of Bacillus subtilis Rel in complex with DarB -

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Basic information

Entry
Database: PDB / ID: 8acu
TitleStructure of Bacillus subtilis Rel in complex with DarB
Components
  • CBS domain-containing protein
  • GTP pyrophosphokinase
KeywordsTRANSFERASE / Rel / GTP pyrophosphokinase / DarB / CBPB / stringent factor / translation / ribosome
Function / homology
Function and homology information


GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation / GTP binding / ATP binding
Similarity search - Function
RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / HD domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain ...RelA/SpoT, AH and RIS domains / RelA/SpoT, AH and RIS domains / HD domain / RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain profile. / ACT domain / ACT-like domain / HD domain profile. / TGS domain profile. / TGS / TGS-like / HD domain / CBS domain superfamily / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
: / CBS domain-containing protein / GTP pyrophosphokinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsGarcia-Pino, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)T.0066.18 Belgium
CitationJournal: To Be Published
Title: Structure of Bacillus subtilis Rel in complex with DarB
Authors: Garcia-Pino, A.
History
DepositionJul 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP pyrophosphokinase
B: GTP pyrophosphokinase
E: CBS domain-containing protein
F: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3756
Polymers120,2654
Non-polymers1102
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-61 kcal/mol
Surface area45630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.401, 98.141, 126.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GTP pyrophosphokinase / (p)ppGpp synthase / ATP:GTP 3'-pyrophosphotransferase / ppGpp synthase I


Mass: 43479.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: relA, BSU27600
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O54408, GTP diphosphokinase
#2: Protein CBS domain-containing protein / Inosine-5'-monophosphate dehydrogenase


Mass: 16653.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3749, Bateq7PJ16_1575, C6Y43_13715, FAL52_03995
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A164SLA6
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293.16 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Magnesium chloride hexahydrate 0.1 M Sodium HEPES 7.5 10 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.97→77.6 Å / Num. obs: 22489 / % possible obs: 95 % / Redundancy: 20.1 % / CC1/2: 0.998 / Rpim(I) all: 0.061 / Net I/σ(I): 11.1
Reflection shellResolution: 2.97→3.08 Å / Num. unique obs: 1023 / CC1/2: 0.387 / Rpim(I) all: 0.851

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S2T

6s2t


Resolution: 2.97→75.72 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3153 1118 4.97 %
Rwork0.2601 --
obs0.2627 22484 89.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.97→75.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7169 0 2 42 7213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.511
X-RAY DIFFRACTIONf_dihedral_angle_d13.6342565
X-RAY DIFFRACTIONf_chiral_restr0.041176
X-RAY DIFFRACTIONf_plane_restr0.0031293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.10.4517740.3491375X-RAY DIFFRACTION47
3.1-3.270.30971210.31442202X-RAY DIFFRACTION76
3.27-3.470.38381330.30622785X-RAY DIFFRACTION96
3.47-3.740.34981360.28552970X-RAY DIFFRACTION100
3.74-4.120.30991720.2512947X-RAY DIFFRACTION100
4.12-4.710.29861370.24422987X-RAY DIFFRACTION100
4.71-5.930.32151740.25292973X-RAY DIFFRACTION100
5.94-75.720.28651710.24363127X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.9521 Å / Origin y: -24.4312 Å / Origin z: 27.0744 Å
111213212223313233
T0.3516 Å2-0.0001 Å2-0.0262 Å2-0.5476 Å20.0333 Å2--0.4923 Å2
L0.4013 °20.6244 °20.268 °2-3.1184 °21.1908 °2--1.5886 °2
S-0.1695 Å °-0.1262 Å °0.0194 Å °-0.1153 Å °0.0561 Å °0.0634 Å °-0.0401 Å °-0.0221 Å °0.108 Å °
Refinement TLS groupSelection details: all

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