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- PDB-6e1v: Crystal structure of a class I PreQ1 riboswitch complexed with a ... -

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Basic information

Entry
Database: PDB / ID: 6e1v
TitleCrystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 3: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine
ComponentsRNA (33-MER)
KeywordsRNA / PreQ1 riboswitch / Synthetic compound / Complex
Function / homologyChem-HMV / RNA / RNA (> 10)
Function and homology information
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 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 2.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: RNA (33-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4782
Polymers10,2241
Non-polymers2541
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-6 kcal/mol
Surface area4970 Å2
Unit cell
Length a, b, c (Å)115.421, 115.421, 58.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: RNA chain RNA (33-MER)


Mass: 10224.107 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
#2: Chemical ChemComp-HMV / 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine


Mass: 254.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 5.17 Å3/Da / Density % sol: 76.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M potassium sodium tartrate, 0.1 M sodium citrate (pH 5.6), 2.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.56→41.09 Å / Num. obs: 7832 / % possible obs: 100 % / Redundancy: 37.7 % / Biso Wilson estimate: 66.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.015 / Rrim(I) all: 0.092 / Net I/σ(I): 29.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.56-2.6738.21.8539280.8580.2981.877100
8.87-41.0929.80.0423810.0080.04199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.56 Å41.09 Å
Translation5.56 Å41.09 Å

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q50

3q50


Resolution: 2.56→41.09 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.32
RfactorNum. reflection% reflection
Rfree0.2475 389 5.01 %
Rwork0.2393 --
obs0.2398 7764 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.78 Å2 / Biso mean: 79.8792 Å2 / Biso min: 24.71 Å2
Refinement stepCycle: final / Resolution: 2.56→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 674 19 2 695
Biso mean--47.96 51.66 -
Num. residues----33
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005774
X-RAY DIFFRACTIONf_angle_d0.9651200
X-RAY DIFFRACTIONf_chiral_restr0.046158
X-RAY DIFFRACTIONf_plane_restr0.0131
X-RAY DIFFRACTIONf_dihedral_angle_d16.708389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5602-2.93050.46361250.462524012526
2.9305-3.69180.27021270.242324012528
3.6918-41.0970.20871370.203325732710
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)
10.5331-0.3921-0.76980.56140.99511.78170.21710.1148-0.1312-0.03080.1431-0.2304-0.1890.15130.03170.7620.27640.17851.0933-0.8361.268940.108737.489426.8441
20.0175-0.15610.08623.8728-0.63590.4307-0.0374-0.0970.19010.7540.0270.4968-0.7007-0.5774-0.1430.9390.1380.21971.0362-0.56951.07340.849341.424319.7698
31.2178-1.4412-2.41672.20632.43425.16540.03090.0145-0.35540.0150.2255-0.45310.21970.28970.13140.70090.12970.01050.898-0.55260.841334.499537.539828.8423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:10)A1 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:15)A11 - 15
3X-RAY DIFFRACTION3(chain A and resid 16:33)A16 - 33

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