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- PDB-6s2u: Structure of the catalytic domain of T. thermophilus Rel in compl... -

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Basic information

Entry
Database: PDB / ID: 6s2u
TitleStructure of the catalytic domain of T. thermophilus Rel in complex with AMP and ppGpp
Components(P)ppGpp synthetase I, SpoT/RelA
KeywordsTRANSFERASE / ppGpp synthetase / ppGpp hydrolase / ppGpp / translation / stringent response
Function / homology
Function and homology information


guanosine tetraphosphate metabolic process / GTP diphosphokinase activity / GTP diphosphokinase
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
ADENOSINE MONOPHOSPHATE / Chem-GN3 / : / trimethylamine oxide / (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: 2.95 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8347
Polymers40,7061
Non-polymers1,1286
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-13 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.739, 50.346, 86.057
Angle α, β, γ (deg.)90.00, 111.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 40705.883 Da / Num. of mol.: 1
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 , 6 types, 27 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GN3 / [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid


Mass: 602.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N6O16P4
#5: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.002 M Zinc chloride 0.1 M Tris 8.0 20 % w/v PEG 6000

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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 9M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.95→56.36 Å / Num. obs: 6572 / % possible obs: 91.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 102.64 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.04 / Net I/σ(I): 13.8
Reflection shellResolution: 2.95→3.02 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 2399 / CC1/2: 0.868 / Rpim(I) all: 0.36

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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: 2.95→56.36 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.528
RfactorNum. reflection% reflectionSelection details
Rfree0.248 330 5.02 %RANDOM
Rwork0.214 ---
obs0.216 6572 63.2 %-
Displacement parametersBiso mean: 101.56 Å2
Baniso -1Baniso -2Baniso -3
1--3.5954 Å20 Å213.1263 Å2
2--0.4492 Å20 Å2
3---3.1462 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.95→56.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 67 20 2681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012715HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.173709HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d921SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes485HARMONIC5
X-RAY DIFFRACTIONt_it2715HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion21.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion360SEMIHARMONIC5
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_contact3056SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.12 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3433 -7.06 %
Rwork0.2312 382 -
all0.2396 411 -
obs--26.06 %
Refinement TLS params.Method: refined / Origin x: 97.0037 Å / Origin y: -62.0508 Å / Origin z: 97.8665 Å
111213212223313233
T-0.3797 Å20.0416 Å20.1468 Å2--0.3284 Å2-0.015 Å2---0.1954 Å2
L6.0815 °2-1.6979 °2-5.5923 °2-1.4825 °21.7601 °2--6.2821 °2
S-0.0439 Å °-0.0675 Å °0.0307 Å °0.2437 Å °-0.0212 Å °-0.1543 Å °-0.0021 Å °-0.1377 Å °0.065 Å °
Refinement TLS groupSelection details: { A|* }

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