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- PDB-8fep: 16mer self-complementary duplex RNA with two continuous native U:... -

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Basic information

Entry
Database: PDB / ID: 8fep
Title16mer self-complementary duplex RNA with two continuous native U:U pairs
ComponentsRNA 16mer
KeywordsRNA / Duplexes / UU pairs
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFang, Z. / 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


Theoretical massNumber of molelcules
Total (without water)5,0601
Polymers5,0601
Non-polymers00
Water99155
1
AAA: RNA 16mer

AAA: RNA 16mer


Theoretical massNumber of molelcules
Total (without water)10,1202
Polymers10,1202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area1490 Å2
ΔGint-13 kcal/mol
Surface area5900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.717, 41.717, 126.234
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-103-

HOH

21AAA-104-

HOH

31AAA-123-

HOH

41AAA-124-

HOH

51AAA-135-

HOH

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Components

#1: RNA chain RNA 16mer


Mass: 5060.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 M Lithium sulfate, 3 % w/v 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033175 Å / Relative weight: 1
ReflectionResolution: 1.55→21.05 Å / Num. obs: 6354 / % possible obs: 98.48 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / Net I/σ(I): 30
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 9 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 310 / CC1/2: 0.994 / Rpim(I) all: 0.066 / Rrim(I) all: 0.199 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→21.048 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.935 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2692 327 5.147 %
Rwork0.2059 6026 -
all0.209 --
obs-6353 98.42 %
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: 25.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0.001 Å20 Å2
2---0.002 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.55→21.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 0 55 389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.012372
X-RAY DIFFRACTIONr_bond_other_d0.0060.018155
X-RAY DIFFRACTIONr_angle_refined_deg2.5481.789577
X-RAY DIFFRACTIONr_angle_other_deg0.7341.655379
X-RAY DIFFRACTIONr_chiral_restr0.2260.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0258
X-RAY DIFFRACTIONr_nbd_refined0.0860.228
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.2146
X-RAY DIFFRACTIONr_nbtor_refined0.2470.2135
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2870.223
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.219
X-RAY DIFFRACTIONr_nbd_other0.3940.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3180.211
X-RAY DIFFRACTIONr_scbond_it2.352.525369
X-RAY DIFFRACTIONr_scbond_other2.3472.524370
X-RAY DIFFRACTIONr_scangle_it2.9423.813577
X-RAY DIFFRACTIONr_scangle_other2.9393.812578
X-RAY DIFFRACTIONr_lrange_it4.47724.274466
X-RAY DIFFRACTIONr_lrange_other4.42424.027463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.248200.208438X-RAY DIFFRACTION100
1.59-1.6340.252230.222434X-RAY DIFFRACTION100
1.634-1.6810.18326419X-RAY DIFFRACTION100
1.681-1.7330.29240.234416X-RAY DIFFRACTION100
1.733-1.7890.304240.222381X-RAY DIFFRACTION100
1.789-1.8520.4220.23381X-RAY DIFFRACTION100
1.852-1.9220.347270.225358X-RAY DIFFRACTION98.2143
1.922-20.265240.227359X-RAY DIFFRACTION100
2-2.0890.229160.216348X-RAY DIFFRACTION100
2.089-2.1910.224190.21335X-RAY DIFFRACTION100
2.191-2.3090.287120.23321X-RAY DIFFRACTION100
2.309-2.4480.22212297X-RAY DIFFRACTION100
2.448-2.6170.37190.231275X-RAY DIFFRACTION99.3243
2.617-2.8260.391150.231260X-RAY DIFFRACTION98.5663
2.826-3.0940.209100.197245X-RAY DIFFRACTION99.6094
3.094-3.4570.38100.178224X-RAY DIFFRACTION96.6942
3.457-3.9870.1488192X-RAY DIFFRACTION96.1538
3.987-4.8720.16710158X-RAY DIFFRACTION91.3044
4.872-6.8450.2240.188123X-RAY DIFFRACTION85.8108
6.845-21.0480.63620.28562X-RAY DIFFRACTION64.6465

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