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- PDB-6dme: ppGpp Riboswitch bound to ppGpp, thallium acetate structure -

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Basic information

Entry
Database: PDB / ID: 6dme
TitleppGpp Riboswitch bound to ppGpp, thallium acetate structure
ComponentsppGpp Riboswitch
KeywordsRNA / riboswitch / non-coding / yKKC
Function / homologyGUANOSINE-5',3'-TETRAPHOSPHATE / THALLIUM (I) ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesSulfobacillus acidophilus DSM 10332 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.702 Å
AuthorsPeselis, A. / Serganov, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112940 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM119357 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM88118 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.
Authors: Peselis, A. / Serganov, A.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_database_PDB_obs_spr / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 27, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ppGpp Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,44016
Polymers33,3171
Non-polymers1,12415
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.184, 51.816, 77.862
Angle α, β, γ (deg.)90.00, 128.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain ppGpp Riboswitch


Mass: 33316.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfobacillus acidophilus DSM 10332 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.075 M MgCl2, 0.1 M Na-acetate pH 4.2, and 21% PEG400 (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1.105 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15858 / % possible obs: 98.4 % / Redundancy: 4.6 % / CC1/2: 0.961 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.049 / Net I/σ(I): 21.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.237 / Num. measured obs: 8587 / Rpim(I) all: 0.129

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.702→27.52 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 27.81
RfactorNum. reflection% reflection
Rfree0.2426 1608 10.14 %
Rwork0.1993 --
obs0.2036 15858 93.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.702→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2203 50 8 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032506
X-RAY DIFFRACTIONf_angle_d0.7823914
X-RAY DIFFRACTIONf_dihedral_angle_d19.8291248
X-RAY DIFFRACTIONf_chiral_restr0.058512
X-RAY DIFFRACTIONf_plane_restr0.003104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7018-2.7890.43551350.37871141X-RAY DIFFRACTION83
2.789-2.88850.32581310.32961261X-RAY DIFFRACTION89
2.8885-3.0040.33271350.26691256X-RAY DIFFRACTION92
3.004-3.14060.28041590.24381295X-RAY DIFFRACTION95
3.1406-3.30590.25321400.2071321X-RAY DIFFRACTION93
3.3059-3.51260.27531550.19481304X-RAY DIFFRACTION96
3.5126-3.78320.19291460.18311308X-RAY DIFFRACTION97
3.7832-4.16280.23821580.15081339X-RAY DIFFRACTION97
4.1628-4.76240.16761540.15691370X-RAY DIFFRACTION98
4.7624-5.990.1831500.14421331X-RAY DIFFRACTION97
5.99-27.52110.23191450.19361324X-RAY DIFFRACTION95

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