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- PDB-7ei8: RNA kink-turn motif with 2-aminopurine -

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Basic information

Entry
Database: PDB / ID: 7ei8
TitleRNA kink-turn motif with 2-aminopurine
ComponentsRNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
KeywordsRNA / Kink-turn motif / 2-aminopurine
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKondo, J. / Saisu, S.
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*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
B: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
C: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
D: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,37618
Polymers24,5514
Non-polymers82514
Water00
1
A: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
B: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5707
Polymers12,2762
Non-polymers2955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-2 kcal/mol
Surface area5530 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
D: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,80611
Polymers12,2762
Non-polymers5309
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-4 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.124, 42.895, 56.269
Angle α, β, γ (deg.)90.000, 116.040, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-101-

CO

21D-101-

CO

31D-103-

CO

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Components

#1: RNA chain
RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))-R(P*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')


Mass: 6137.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Co
Has ligand of interestY
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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, hexammine cobalt, MPD, potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.60499 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60499 Å / Relative weight: 1
ReflectionResolution: 3.1→48.26 Å / Num. obs: 4510 / % possible obs: 97.1 % / Redundancy: 6.499 % / Biso Wilson estimate: 73.411 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 0.942 / Net I/σ(I): 17 / Num. measured all: 29309
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
3.1-3.186.610.3344.4821553363260.9680.36297
3.18-3.276.3890.2555.4420513343210.990.27796.1
3.27-3.376.5670.1758.1720953313190.990.1996.4
3.37-3.476.5680.1558.9318262892780.9950.16996.2
3.47-3.587.0230.12911.6621773193100.9950.13997.2
3.58-3.716.8460.12311.2318692832730.9970.13496.5
3.71-3.856.9550.09813.7219962962870.9980.10697
3.85-4.016.7160.08517.1717732692640.9980.09298.1
4.01-4.186.3840.08117.4615452512420.9970.08996.4
4.18-4.396.5240.07121.2716572612540.9970.07897.3
4.39-4.636.7070.07220.4815362332290.9980.07898.3
4.63-4.916.7030.07222.4814882272220.9970.07897.8
4.91-5.256.680.05327.3813762122060.9980.05897.2
5.25-5.676.3470.05428.7212441991960.9970.05998.5
5.67-6.215.8990.05227.0411091941880.9980.05896.9
6.21-6.946.0490.04928.339801651620.9970.05498.2
6.94-8.016.020.0528.659091521510.9980.05499.3
8.01-9.815.3470.04429.7164712512110.04996.8
9.81-13.885.3660.04430.795421021010.9990.04999
13.88-48.265.5670.03832.66334656010.04192.3

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Processing

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

4c40


Resolution: 3.1→48.26 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 455 10.14 %
Rwork0.1963 4031 -
obs0.2026 4486 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.46 Å2 / Biso mean: 68.1413 Å2 / Biso min: 42.54 Å2
Refinement stepCycle: final / Resolution: 3.1→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1632 14 0 1646
Biso mean--92.55 --
Num. residues----76
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.550.34291420.24581330147296
3.55-4.470.29171560.21521320147697
4.47-48.260.21911570.17061381153898

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