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- PDB-6s2t: Structure of the N-terminal catalytic region of T. thermophilus R... -

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Basic information

Entry
Database: PDB / ID: 6s2t
TitleStructure of the N-terminal catalytic region of T. thermophilus Rel bound to ppGpp
Components(P)ppGpp synthetase I, SpoT/RelA
KeywordsTRANSFERASE / ppGpp hydrolase / ppGpp synthetase / Rel / ppGpp
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
GUANOSINE-5',3'-TETRAPHOSPHATE / : / (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: 2.75 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 / Derived calculations / Refinement description
Category: citation / software / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,6318
Polymers40,7061
Non-polymers9257
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-31 kcal/mol
Surface area16980 Å2
Unit cell
Length a, b, c (Å)87.927, 87.927, 184.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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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 BL21(DE3) (bacteria)
References: UniProt: F6DES6, UniProt: Q5SHL3*PLUS, GTP diphosphokinase

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Non-polymers , 7 types, 121 molecules

#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.44 Å3/Da / Density % sol: 72.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate, Sodium HEPES; MOPS (acid) pH 7.5, 25% ...Details: 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate, Sodium HEPES; MOPS (acid) pH 7.5, 25% v/v MPD; 25% PEG 1000; 25% 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 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 2.75→92.13 Å / Num. obs: 14292 / % possible obs: 99.8 % / Redundancy: 24.8 % / Biso Wilson estimate: 90.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.041 / Rrim(I) all: 0.204 / Net I/σ(I): 13.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 22.6 % / Rmerge(I) obs: 2.452 / Num. unique obs: 2751 / CC1/2: 0.627 / Rpim(I) all: 0.522 / Rrim(I) all: 2.508 / % possible all: 98.9

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJ7

1vj7


Resolution: 2.75→62.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.647 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.8 / SU Rfree Blow DPI: 0.31 / SU Rfree Cruickshank DPI: 0.305
RfactorNum. reflection% reflectionSelection details
Rfree0.22 716 5.07 %RANDOM
Rwork0.196 ---
obs0.197 14116 72 %-
Displacement parametersBiso max: 174.03 Å2 / Biso mean: 81.28 Å2 / Biso min: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1-4.9952 Å20 Å20 Å2
2--4.9952 Å20 Å2
3----9.9904 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.75→62.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 52 116 2899
Biso mean--137.41 62.34 -
Num. residues----350
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d987SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes5HARMONIC2
X-RAY DIFFRACTIONt_gen_planes506HARMONIC5
X-RAY DIFFRACTIONt_it2840HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion370SEMIHARMONIC5
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_contact3325SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2840HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg3860HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion20.82
LS refinement shellResolution: 2.75→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 35
RfactorNum. reflection% reflection
Rfree0.3314 24 5.94 %
Rwork0.2429 380 -
all0.2489 404 -
obs--16.65 %
Refinement TLS params.Method: refined / Origin x: 65.923 Å / Origin y: 49.4166 Å / Origin z: 19.3346 Å
111213212223313233
T-0.1521 Å2-0.023 Å20.091 Å2-0.0411 Å2-0.004 Å2---0.2106 Å2
L1.0409 °2-0.089 °2-1.494 °2-1.1512 °20.4203 °2--4.0524 °2
S0.3131 Å °0.0701 Å °0.3566 Å °0.2086 Å °-0.0353 Å °-0.0224 Å °-0.4737 Å °0.2241 Å °-0.2778 Å °
Refinement TLS groupSelection details: { A|* }

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