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- PDB-6dnr: PRPP Riboswitch bound to PRPP, ligand-free structure -

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Basic information

Entry
Database: PDB / ID: 6dnr
TitlePRPP Riboswitch bound to PRPP, ligand-free structure
ComponentsPRPP Riboswitch
KeywordsRNA / riboswitch / non-coding / yKKC
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesSyntrophothermus lipocalidus DSM 12680 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.896 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 7, 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 / Derived calculations
Category: database_2 / pdbx_database_PDB_obs_spr ...database_2 / pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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Assembly

Deposited unit
A: PRPP Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9754
Polymers34,9031
Non-polymers733
Water00
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)63.773, 63.773, 376.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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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: 3.17 Å3/Da / Density % sol: 61.15 %
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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.89→20 Å / Num. obs: 10251 / % possible obs: 93.8 % / Redundancy: 9.5 % / CC1/2: 0.834 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.051 / Net I/σ(I): 27.6
Reflection shellResolution: 2.9→2.95 Å / Rmerge(I) obs: 1.554 / Rpim(I) all: 0.388

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.896→19.807 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.96
RfactorNum. reflection% reflection
Rfree0.2734 1028 10.03 %
Rwork0.2121 --
obs0.2185 10251 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.896→19.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2310 3 0 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062584
X-RAY DIFFRACTIONf_angle_d1.2414035
X-RAY DIFFRACTIONf_dihedral_angle_d20.2391293
X-RAY DIFFRACTIONf_chiral_restr0.054533
X-RAY DIFFRACTIONf_plane_restr0.008108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8961-3.04820.42451450.35831296X-RAY DIFFRACTION96
3.0482-3.23840.3381480.28681331X-RAY DIFFRACTION97
3.2384-3.48720.36251500.24071341X-RAY DIFFRACTION98
3.4872-3.83590.34041530.24021363X-RAY DIFFRACTION98
3.8359-4.38570.31031520.22461359X-RAY DIFFRACTION97
4.3857-5.50580.26531430.20781303X-RAY DIFFRACTION89
5.5058-19.80780.21691370.17791230X-RAY DIFFRACTION78
Refinement TLS params.Method: refined / Origin x: -27.656 Å / Origin y: 1.1008 Å / Origin z: -31.1645 Å
111213212223313233
T1.2944 Å20.0256 Å2-0.0021 Å2-0.8735 Å2-0.0605 Å2--0.6058 Å2
L1.7159 °20.4227 °20.7156 °2-4.4018 °20.0417 °2--0.3931 °2
S0.2346 Å °0.3327 Å °0.0204 Å °-0.28 Å °-0.2261 Å °-0.0079 Å °0.51 Å °-0.2031 Å °0.0114 Å °
Refinement TLS groupSelection details: all

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