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- PDB-8feq: 16mer self-complementary duplex RNA with two separated s(2)U:s(2)... -

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Basic information

Entry
Database: PDB / ID: 8feq
Title16mer self-complementary duplex RNA with two separated s(2)U:s(2)U pairs
ComponentsRNA 16mer with two separated s(2)U
KeywordsRNA / Duplexes / UU pairs / 2-thio-U
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsFang, Z. / Zhou, L. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Simons Foundation290363FY18 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying.
Authors: Ding, D. / Fang, Z. / Kim, S.C. / O'Flaherty, D.K. / Jia, X. / Stone, T.B. / Zhou, L. / Szostak, J.W.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Feb 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: RNA 16mer with two separated s(2)U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1322
Polymers5,0921
Non-polymers401
Water97354
1
AAA: RNA 16mer with two separated s(2)U
hetero molecules

AAA: RNA 16mer with two separated s(2)U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2644
Polymers10,1842
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3940 Å2
ΔGint-26 kcal/mol
Surface area5410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.261, 41.261, 124.239
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-222-

HOH

21AAA-232-

HOH

31AAA-239-

HOH

41AAA-244-

HOH

51AAA-252-

HOH

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Components

#1: RNA chain RNA 16mer with two separated s(2)U


Mass: 5092.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.075 M Sodium chloride, 0.002 M Calcium chloride dihydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 30% w/v 1,6 Hexanediol, 0.0005 M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.03769 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03769 Å / Relative weight: 1
ReflectionResolution: 1.5→31 Å / Num. obs: 6853 / % possible obs: 100 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.029 / Rrim(I) all: 0.082 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 352 / CC1/2: 0.973 / Rpim(I) all: 0.081 / Rrim(I) all: 0.249 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.993 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.502 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2103 328 4.79 %
Rwork0.1774 6520 -
all0.179 --
obs-6848 99.883 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.009 Å2-0.004 Å20 Å2
2---0.009 Å20 Å2
3---0.028 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 1 54 389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.013373
X-RAY DIFFRACTIONr_bond_other_d0.0440.02161
X-RAY DIFFRACTIONr_angle_refined_deg2.5771.909561
X-RAY DIFFRACTIONr_angle_other_deg3.9681.923389
X-RAY DIFFRACTIONr_chiral_restr0.1960.275
X-RAY DIFFRACTIONr_chiral_restr_other2.5190.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.02181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0258
X-RAY DIFFRACTIONr_nbd_refined0.1090.228
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.2164
X-RAY DIFFRACTIONr_nbtor_refined0.2380.2144
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.292
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.222
X-RAY DIFFRACTIONr_metal_ion_refined0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.219
X-RAY DIFFRACTIONr_nbd_other0.3820.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.214
X-RAY DIFFRACTIONr_scbond_it1.5521.799372
X-RAY DIFFRACTIONr_scbond_other1.551.798373
X-RAY DIFFRACTIONr_scangle_it2.0122.713560
X-RAY DIFFRACTIONr_scangle_other2.012.713561
X-RAY DIFFRACTIONr_lrange_it3.29717.235472
X-RAY DIFFRACTIONr_lrange_other3.31217.216472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.229230.224500X-RAY DIFFRACTION99.8092
1.539-1.5810.25190.207449X-RAY DIFFRACTION99.5745
1.581-1.6270.224250.213432X-RAY DIFFRACTION100
1.627-1.6770.194280.17422X-RAY DIFFRACTION100
1.677-1.7320.24170.169437X-RAY DIFFRACTION100
1.732-1.7930.271220.161418X-RAY DIFFRACTION100
1.793-1.860.197190.176388X-RAY DIFFRACTION100
1.86-1.9360.204240.175365X-RAY DIFFRACTION99.4885
1.936-2.0220.229180.177360X-RAY DIFFRACTION100
2.022-2.120.224170.181361X-RAY DIFFRACTION100
2.12-2.2350.263170.189330X-RAY DIFFRACTION100
2.235-2.370.249190.168321X-RAY DIFFRACTION100
2.37-2.5330.316130.199308X-RAY DIFFRACTION100
2.533-2.7350.215180.208280X-RAY DIFFRACTION100
2.735-2.9950.238130.189263X-RAY DIFFRACTION100
2.995-3.3460.18250.158237X-RAY DIFFRACTION100
3.346-3.8590.215120.16213X-RAY DIFFRACTION100
3.859-4.7160.123120.153187X-RAY DIFFRACTION100
4.716-6.6270.33540.161150X-RAY DIFFRACTION99.3548
6.627-30.9930.04530.20799X-RAY DIFFRACTION98.0769

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