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- PDB-6e1w: Crystal structure of a class I PreQ1 riboswitch complexed with PreQ1 -

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Basic information

Entry
Database: PDB / ID: 6e1w
TitleCrystal structure of a class I PreQ1 riboswitch complexed with PreQ1
ComponentsRNA (33-MER)
KeywordsRNA / PreQ1 riboswitch / Synthetic compound / Complex
Function / homologyACETATE ION / Chem-HNG / RNA / RNA (> 10)
Function and homology information
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsNumata, T. / Connelly, C.M. / Schneekloth, J.S. / Ferre-D'Amare, A.R.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2019
Title: Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Authors: Connelly, C.M. / Numata, T. / Boer, R.E. / Moon, M.H. / Sinniah, R.S. / Barchi, J.J. / Ferre-D'Amare, A.R. / Schneekloth Jr., J.S.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Dec 4, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code / _pdbx_audit_support.funding_organization
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6555
Polymers10,3331
Non-polymers3224
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-10 kcal/mol
Surface area5420 Å2
Unit cell
Length a, b, c (Å)52.297, 52.297, 179.215
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: RNA chain RNA (33-MER)


Mass: 10333.194 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
#2: Chemical ChemComp-HNG / 2-amino-5-(aminomethyl)-1,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / PreQ1


Mass: 179.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.01 M magnesium acetate, 0.05 M MES (pH 5.6), 2.7 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→44.8 Å / Num. obs: 17169 / % possible obs: 99.6 % / Redundancy: 33.2 % / Biso Wilson estimate: 38.24 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.006 / Rrim(I) all: 0.037 / Net I/σ(I): 44.4 / Num. measured all: 569211 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.69-1.72191.4117830.6710.3261.4596.2
9.1-44.823.20.02516510.0060.02699.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.09 Å43.91 Å
Translation5.09 Å43.91 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→43.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.8
RfactorNum. reflection% reflection
Rfree0.2101 854 5 %
Rwork0.1805 --
obs0.182 17086 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.99 Å2 / Biso mean: 49.1728 Å2 / Biso min: 33.21 Å2
Refinement stepCycle: final / Resolution: 1.69→43.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 675 22 96 793
Biso mean--45.53 55.02 -
Num. residues----33
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005773
X-RAY DIFFRACTIONf_angle_d0.9891197
X-RAY DIFFRACTIONf_chiral_restr0.046157
X-RAY DIFFRACTIONf_plane_restr0.01234
X-RAY DIFFRACTIONf_dihedral_angle_d13.066379
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.79590.27011340.26462551268597
1.7959-1.93460.27841390.251426362775100
1.9346-2.12930.25551390.246126532792100
2.1293-2.43730.3181430.246226982841100
2.4373-3.07070.25161430.236927482891100
3.0707-43.92490.17351560.141629463102100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8696-2.07991.10687.89610.42074.6023-0.1043-0.00330.07170.25220.1695-0.56140.70550.3837-0.0550.4020.15780.06790.51630.02960.378237.666838.249130.0324
22.92420.84231.58179.63772.49316.5778-0.00440.10790.9372-0.3537-0.0113-0.6283-0.08440.3245-0.03480.52250.07780.05970.3926-0.03850.449138.25334.816220.0569
38.34783.51222.99782.23860.7652.5224-0.0254-0.3598-0.03360.2219-0.2430.18110.35940.01250.24480.35830.08580.04740.5416-0.0270.385232.11745.092936.3141
43.6764-2.1123-1.85758.34036.09354.4818-0.1627-0.095-0.21240.6937-0.16650.53481.3995-0.09570.42390.56220.06310.04580.35840.0080.393334.314830.662326.7568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:8)A1 - 8
2X-RAY DIFFRACTION2(chain A and resid 9:16)A9 - 16
3X-RAY DIFFRACTION3(chain A and resid 17:23)A17 - 23
4X-RAY DIFFRACTION4(chain A and resid 24:33)A24 - 33

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