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

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Basic information

Entry
Database: PDB / ID: 7eia
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 / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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')
C: 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')
D: 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')
E: 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')
F: 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')
G: 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')
H: 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)50,05013
Polymers49,8558
Non-polymers1955
Water00
1
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)12,5424
Polymers12,4642
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-8 kcal/mol
Surface area6320 Å2
MethodPISA
2
C: 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')
D: 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)12,5424
Polymers12,4642
Non-polymers782
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-12 kcal/mol
Surface area6320 Å2
MethodPISA
3
E: 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')
F: 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')


Theoretical massNumber of molelcules
Total (without water)12,4642
Polymers12,4642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint1 kcal/mol
Surface area6530 Å2
MethodPISA
4
G: 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')
H: 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)12,5033
Polymers12,4642
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-2 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.056, 77.575, 81.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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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.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, potassium 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: Feb 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→43.51 Å / Num. obs: 8773 / % possible obs: 95.7 % / Redundancy: 3.33 % / Biso Wilson estimate: 84.303 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.047 / Χ2: 0.936 / Net I/σ(I): 18.3 / Num. measured all: 29217
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
3-3.13.3910.3832.6826868277920.9270.44995.8
3.1-3.23.3480.2274.324147367210.9820.26798
3.2-3.33.2870.1555.8921536646550.990.18398.6
3.3-3.43.1480.127.7417635645600.9930.14399.3
3.4-3.52.950.1218.1414695164980.990.14696.5
3.5-43.4190.06814.246294189018410.9970.0897.4
4-53.4940.03925.146327187718110.9980.04596.5
5-43.513.2250.02437.636111209418950.9990.02890.5

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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: 3→43.51 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 889 10.17 %
Rwork0.2003 7850 -
obs0.2073 8739 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.91 Å2 / Biso mean: 78.2786 Å2 / Biso min: 33.03 Å2
Refinement stepCycle: final / Resolution: 3→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3312 5 0 3317
Biso mean--93.4 --
Num. residues----152
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 (%)
3-3.190.35641410.27451294143598
3.19-3.440.32531510.24031320147198
3.44-3.780.27631460.21331298144497
3.78-4.330.30261540.20651318147297
4.33-5.450.25881500.19431316146696
5.45-43.510.2281470.17651304145189

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