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- PDB-6s2v: Structure of the N-terminal catalytic region of T. thermophilus Rel -

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Basic information

Entry
Database: PDB / ID: 6s2v
TitleStructure of the N-terminal catalytic region of T. thermophilus Rel
Components(P)ppGpp synthetase I, SpoT/RelA
KeywordsTRANSFERASE / ppGpp hydrolase / ppGpp synthetase / ppGpp / stringent response / translation
Function / homology
Function and homology information


guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / GTP diphosphokinase / nucleotide binding / metal ion 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 / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / (P)ppGpp synthetase I, SpoT/RelA / Guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase (PpGpp synthase)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsGarcia-Pino, A.
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: A nucleotide-switch mechanism mediates opposing catalytic activities of Rel enzymes.
Authors: Tamman, H. / Van Nerom, K. / Takada, H. / Vandenberk, N. / Scholl, D. / Polikanov, Y. / Hofkens, J. / Talavera, A. / Hauryliuk, V. / Hendrix, J. / Garcia-Pino, A.
History
DepositionJun 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 29, 2020Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.name
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (P)ppGpp synthetase I, SpoT/RelA
B: (P)ppGpp synthetase I, SpoT/RelA
C: (P)ppGpp synthetase I, SpoT/RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,82614
Polymers122,3313
Non-polymers49511
Water1,13563
1
A: (P)ppGpp synthetase I, SpoT/RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8673
Polymers40,7771
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (P)ppGpp synthetase I, SpoT/RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9624
Polymers40,7771
Non-polymers1853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (P)ppGpp synthetase I, SpoT/RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9977
Polymers40,7771
Non-polymers2206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.737, 105.737, 241.455
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein (P)ppGpp synthetase I, SpoT/RelA


Mass: 40776.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: Ththe16_1734 / Production host: Escherichia coli (E. coli)
References: UniProt: F6DES6, UniProt: Q5SHL3*PLUS, GTP diphosphokinase

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Non-polymers , 5 types, 74 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium bromide 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.96→40.77 Å / Num. obs: 21371 / % possible obs: 93.7 % / Redundancy: 13.9 % / Biso Wilson estimate: 104.77 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.06 / Net I/σ(I): 14.38
Reflection shellResolution: 2.96→3.12 Å / Rmerge(I) obs: 1.69 / Num. unique obs: 401 / CC1/2: 0.611 / Rpim(I) all: 0.52

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vj7

1vj7


Resolution: 2.96→40.77 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.533
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1066 5.01 %RANDOM
Rwork0.221 ---
obs0.224 21292 72.4 %-
Displacement parametersBiso mean: 101.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.8019 Å20 Å20 Å2
2---1.8019 Å20 Å2
3---3.6037 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.96→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7489 0 15 62 7566
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017658HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1810448HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2549SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1309HARMONIC5
X-RAY DIFFRACTIONt_it7658HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.29
X-RAY DIFFRACTIONt_other_torsion22.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1048SEMIHARMONIC5
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_contact8867SEMIHARMONIC4
LS refinement shellResolution: 2.96→3.12 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3075 -5.87 %
Rwork0.2696 401 -
all0.272 426 -
obs--10.44 %
Refinement TLS params.Method: refined / Origin x: 52.8994 Å / Origin y: 1.2847 Å / Origin z: 0.7477 Å
111213212223313233
T-0.0561 Å2-0.1687 Å2-0.0616 Å2--0.1182 Å20.1043 Å2---0.0639 Å2
L0.5435 °2-0.7256 °20.321 °2-0.5584 °2-0.1097 °2--0.8055 °2
S-0.0688 Å °-0.0119 Å °-0.0838 Å °-0.0922 Å °0.1108 Å °-0.0042 Å °-0.0135 Å °0.0924 Å °-0.042 Å °
Refinement TLS groupSelection details: { *|* }

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