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- PDB-6dls: PRPP Riboswitch bound to PRPP, thallium acetate soaked structure -

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Basic information

Entry
Database: PDB / ID: 6dls
TitlePRPP Riboswitch bound to PRPP, thallium acetate soaked structure
ComponentsPRPP Riboswitch
KeywordsRNA / riboswitch / non-coding / yKKC
Function / homologyChem-PRP / THALLIUM (I) ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesSyntrophothermus lipocalidus DSM 12680 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.885 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 2, 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Apr 27, 2022Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_database_PDB_obs_spr
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRPP Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5706
Polymers34,9031
Non-polymers6675
Water181
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)85.220, 91.977, 75.058
Angle α, β, γ (deg.)90.00, 122.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain PRPP Riboswitch


Mass: 34902.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Syntrophothermus lipocalidus DSM 12680 (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O14P3 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Tl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NH4-acetate, 0.1 M HEPES-KOH pH 7.4, and 45% 2-methyl-2,4-pentanediol (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.885→20 Å / Num. obs: 19937 / % possible obs: 97.9 % / Redundancy: 4.8 % / CC1/2: 0.726 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.05 / Net I/σ(I): 28.2
Reflection shellResolution: 2.9→19.35 Å / Rmerge(I) obs: 0.826 / Rpim(I) all: 0.454

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.885→19.35 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 30.81
RfactorNum. reflection% reflection
Rfree0.2348 1974 9.9 %
Rwork0.207 --
obs0.2097 19937 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.885→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2310 26 1 2337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012606
X-RAY DIFFRACTIONf_angle_d1.44070
X-RAY DIFFRACTIONf_dihedral_angle_d19.461298
X-RAY DIFFRACTIONf_chiral_restr0.055537
X-RAY DIFFRACTIONf_plane_restr0.008108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8847-2.95660.44091030.43121064X-RAY DIFFRACTION76
2.9566-3.03630.4471150.38571197X-RAY DIFFRACTION87
3.0363-3.12530.39571670.3491245X-RAY DIFFRACTION90
3.1253-3.22570.37121410.3121275X-RAY DIFFRACTION93
3.2257-3.34040.36581510.25711314X-RAY DIFFRACTION96
3.3404-3.47340.30081510.23421304X-RAY DIFFRACTION96
3.4734-3.63050.30691590.22821353X-RAY DIFFRACTION98
3.6305-3.82050.2421410.22541363X-RAY DIFFRACTION97
3.8205-4.05790.22851600.21481317X-RAY DIFFRACTION96
4.0579-4.36780.25161290.20351341X-RAY DIFFRACTION96
4.3678-4.80130.25341380.20321320X-RAY DIFFRACTION94
4.8013-5.48220.18141460.17811264X-RAY DIFFRACTION93
5.4822-6.85560.22061290.18011330X-RAY DIFFRACTION94
6.8556-19.35030.1571440.15871276X-RAY DIFFRACTION91

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