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- PDB-7f8z: RNA kink-turn motif with 2-aminopurine -

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Basic information

Entry
Database: PDB / ID: 7f8z
TitleRNA kink-turn motif with 2-aminopurine
ComponentsRNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
KeywordsRNA / 2-aminopurine / kink-turn motif
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
DepositionJul 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 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*(2PR))-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*(2PR))-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*(2PR))-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*(2PR))-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*(2PR))-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*(2PR))-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*(2PR))-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*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
I: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
J: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-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)62,37415
Polymers62,17810
Non-polymers1955
Water19811
1
A: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-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*(2PR))-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)12,4753
Polymers12,4362
Non-polymers391
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-4 kcal/mol
Surface area6480 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-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*(2PR))-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)12,4753
Polymers12,4362
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-1 kcal/mol
Surface area6500 Å2
MethodPISA
3
E: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-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*(2PR))-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)12,4753
Polymers12,4362
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-5 kcal/mol
Surface area6480 Å2
MethodPISA
4
G: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-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*(2PR))-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)12,4753
Polymers12,4362
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-1 kcal/mol
Surface area6400 Å2
MethodPISA
5
I: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-R(P*GP*AP*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
J: RNA (5'-R(*GP*GP*CP*GP*A)-D(P*(2PR))-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)12,4753
Polymers12,4362
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-1 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.962, 87.726, 124.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 6217.834 Da / Num. of mol.: 10 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 2.89 Å3/Da / Density % sol: 57.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 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 EIGER2 X 16M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→35.04 Å / Num. obs: 14856 / % possible obs: 98.7 % / Redundancy: 5.796 % / Biso Wilson estimate: 44.299 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.109 / Χ2: 0.922 / Net I/σ(I): 14.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.15.8520.3965.2313480.9450.43699.2
3.1-3.25.8920.2816.9112180.9830.30999.4
3.2-3.35.7910.2138.510670.9840.23599.3
3.3-3.45.5820.15810.59160.9880.17498.7
3.4-3.55.1050.14410.688310.9890.16198
3.5-46.0180.12313.4130640.9940.13698.9
4-56.0980.08917.6430740.9950.09799.4
5-1005.4870.0523.8733070.9980.05597.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C40

4c40


Resolution: 3→35.04 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1485 10 %
Rwork0.1757 13371 -
obs0.1809 14856 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.3 Å2 / Biso mean: 35.2233 Å2 / Biso min: 15.53 Å2
Refinement stepCycle: final / Resolution: 3→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4130 5 11 4146
Biso mean--80.15 29.28 -
Num. residues----190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.99-3.090.29011260.25181130125695
3.09-3.20.26991360.21661217135399
3.2-3.330.29021320.20391200133299
3.33-3.480.24811330.19811199133298
3.48-3.660.27331350.19671219135498
3.66-3.890.25341310.17521193132499
3.89-4.190.23351360.165512231359100
4.19-4.610.21511380.1541228136699
4.61-5.280.21211360.1661229136599
5.28-6.640.17861400.13971262140299
6.64-35.040.18271420.16261271141395

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