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

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Basic information

Entry
Database: PDB / ID: 8fer
Title16mer self-complementary duplex RNA with two continuous s(2)U:s(2)U pairs
ComponentsRNA 16mer with two continuous 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: 1.54 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

Downloads & links

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Assembly

Deposited unit
AAA: RNA 16mer with two continuous s(2)U
BBB: RNA 16mer with two continuous s(2)U


Theoretical massNumber of molelcules
Total (without water)10,1842
Polymers10,1842
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.810, 43.810, 258.170
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-106-

HOH

21AAA-108-

HOH

31AAA-112-

HOH

41AAA-132-

HOH

51AAA-136-

HOH

61AAA-138-

HOH

71AAA-143-

HOH

81AAA-146-

HOH

91BBB-109-

HOH

101BBB-110-

HOH

111BBB-121-

HOH

121BBB-124-

HOH

131BBB-129-

HOH

141BBB-135-

HOH

151BBB-137-

HOH

161BBB-139-

HOH

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Components

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


Mass: 5092.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M Magnesium chloride hexahydrate, 0.002 M Cobalt(II) chloride hexahydrate, 0.05 M HEPES sodium pH 7.5, 2.0 M Ammonium sulfate, 0.001 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: 1.54→50 Å / Num. obs: 14744 / % possible obs: 99.7 % / Redundancy: 7.9 % / CC1/2: 0.986 / CC star: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.043 / Rrim(I) all: 0.121 / Χ2: 0.911 / Net I/σ(I): 13.7
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 747 / CC1/2: 0.978 / CC star: 0.994 / Rpim(I) all: 0.166 / Rrim(I) all: 0.461 / Χ2: 0.505 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→43.065 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 1.576 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2587 725 5.098 %
Rwork0.2187 13496 -
all0.221 --
obs-14221 96.101 %
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: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20.001 Å2-0 Å2
2--0.002 Å2-0 Å2
3----0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.54→43.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 668 0 85 753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.013744
X-RAY DIFFRACTIONr_bond_other_d0.0310.02320
X-RAY DIFFRACTIONr_angle_refined_deg2.7571.9141130
X-RAY DIFFRACTIONr_angle_other_deg3.8731.92776
X-RAY DIFFRACTIONr_chiral_restr0.1830.2152
X-RAY DIFFRACTIONr_chiral_restr_other2.0280.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02116
X-RAY DIFFRACTIONr_nbd_refined0.1510.274
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2490.2373
X-RAY DIFFRACTIONr_nbtor_refined0.2490.2279
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1290.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.238
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.26
X-RAY DIFFRACTIONr_nbd_other0.1850.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1230.218
X-RAY DIFFRACTIONr_scbond_it1.5931.467743
X-RAY DIFFRACTIONr_scbond_other1.5921.467744
X-RAY DIFFRACTIONr_scangle_it2.2162.2181129
X-RAY DIFFRACTIONr_scangle_other2.2152.2181130
X-RAY DIFFRACTIONr_lrange_it3.24913.897945
X-RAY DIFFRACTIONr_lrange_other3.24813.832943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.344420.244729X-RAY DIFFRACTION71.2569
1.58-1.6230.339430.247912X-RAY DIFFRACTION91.126
1.623-1.670.298470.229924X-RAY DIFFRACTION97.1
1.67-1.7210.232520.214919X-RAY DIFFRACTION97.9818
1.721-1.7780.202620.204875X-RAY DIFFRACTION99.1534
1.778-1.840.244460.21894X-RAY DIFFRACTION99.3658
1.84-1.910.212470.225856X-RAY DIFFRACTION99.8894
1.91-1.9880.281450.237820X-RAY DIFFRACTION99.6544
1.988-2.0760.243450.214770X-RAY DIFFRACTION99.2692
2.076-2.1770.201330.21774X-RAY DIFFRACTION99.8762
2.177-2.2950.223400.216717X-RAY DIFFRACTION99.8681
2.295-2.4340.276350.215685X-RAY DIFFRACTION99.4475
2.434-2.6020.307340.226636X-RAY DIFFRACTION99.851
2.602-2.810.206260.237611X-RAY DIFFRACTION99.376
2.81-3.0780.224270.245547X-RAY DIFFRACTION97.619
3.078-3.4410.284290.239494X-RAY DIFFRACTION94.5751
3.441-3.9720.346240.204434X-RAY DIFFRACTION95.4167
3.972-4.8620.188250.165389X-RAY DIFFRACTION98.1043
4.862-6.8650.527130.181314X-RAY DIFFRACTION98.1982
6.865-43.0650.27100.261196X-RAY DIFFRACTION95.814

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