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- PDB-7ei9: RNA kink-turn motif with pyrrolo cytosine -

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Basic information

Entry
Database: PDB / ID: 7ei9
TitleRNA kink-turn motif with pyrrolo cytosine
ComponentsRNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
KeywordsRNA / kink-turn motif / pyrrolo cytosine
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKondo, J. / Miyauchi, T.
CitationJournal: NAR Mol Med / Year: 2025
Title: Structure-based design of a sequence-specific RNA probe that mimics the kink-turn motif
Authors: Miyauchi, T. / Yamaguchi, K. / Saisu, S. / Kondo, J.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
B: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,42813
Polymers12,4642
Non-polymers96411
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-72 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.416, 76.416, 41.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-104-

SR

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Components

#1: RNA chain RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(4PC))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')


Mass: 6231.857 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Sr
Has ligand of interestN
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, strontium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→36.26 Å / Num. obs: 3622 / % possible obs: 99.3 % / Redundancy: 4.142 % / Biso Wilson estimate: 72.438 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.041 / Χ2: 0.953 / Net I/σ(I): 22.76 / Num. measured all: 15002
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.84.430.3973.616173653650.9040.451100
2.8-2.94.4780.1966.8614243183180.9870.222100
2.9-34.3940.1668.0512042742740.9830.188100
3-44.1870.05919.496281150815000.9980.06799.5
4-53.9610.03135.9721595495450.9990.03699.3
5-36.263.7370.01945231763362010.02297.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C40

4c40


Resolution: 2.7→36.26 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 363 10.03 %
Rwork0.2267 3256 -
obs0.229 3619 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.73 Å2 / Biso mean: 60.2245 Å2 / Biso min: 27.6 Å2
Refinement stepCycle: final / Resolution: 2.7→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 828 11 0 839
Biso mean--106.5 --
Num. residues----38
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
2.7-3.090.33151170.317310531170
3.09-3.890.2651190.240510661185
3.89-36.260.22231270.203211371264

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