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- PDB-8te0: 16mer self-complementary duplex RNA with D:C pair sequence 1 -

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Basic information

Entry
Database: PDB / ID: 8te0
Title16mer self-complementary duplex RNA with D:C pair sequence 1
ComponentsRNA
KeywordsRNA / Diaminopurine / Non-canonical base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsFang, Z. / Jia, X. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2104708 United States
Simons Foundation290363 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Diaminopurine in Nonenzymatic RNA Template Copying.
Authors: Jia, X. / Fang, Z. / Kim, S.C. / Ding, D. / Zhou, L. / Szostak, J.W.
History
DepositionJul 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1212
Polymers5,0971
Non-polymers241
Water1,42379
1
A: RNA
hetero molecules

A: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2434
Polymers10,1942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area2980 Å2
ΔGint-15 kcal/mol
Surface area5530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.501, 42.501, 129.967
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
11A-234-

HOH

21A-250-

HOH

31A-252-

HOH

41A-253-

HOH

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Components

#1: RNA chain RNA


Mass: 5097.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 mM Magnesium chloride hexahydrate, 50 mM HEPES sodium pH 7.0, 4.0 M Lithium chloride

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.033216 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033216 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 8586 / % possible obs: 96.2 % / Redundancy: 7.1 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Rrim(I) all: 0.069 / Χ2: 0.919 / Net I/σ(I): 30
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 267 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.214 / Rrim(I) all: 0.345 / Χ2: 0.804 / % possible all: 64.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→35.414 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.485 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2376 379 4.645 %
Rwork0.2146 7781 -
all0.216 --
obs-8160 91.398 %
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: 11.558 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0.001 Å2-0 Å2
2---0.001 Å2-0 Å2
3---0.004 Å2
Refinement stepCycle: LAST / Resolution: 1.42→35.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 337 1 79 417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011374
X-RAY DIFFRACTIONr_bond_other_d0.0020.019157
X-RAY DIFFRACTIONr_angle_refined_deg2.371.906576
X-RAY DIFFRACTIONr_angle_other_deg0.6371.741381
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.575511
X-RAY DIFFRACTIONr_chiral_restr0.0990.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0261
X-RAY DIFFRACTIONr_nbd_refined0.4260.254
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.2173
X-RAY DIFFRACTIONr_nbtor_refined0.2510.2138
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3010.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0810.223
X-RAY DIFFRACTIONr_nbd_other0.1170.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0640.217
X-RAY DIFFRACTIONr_scbond_it1.5981.364374
X-RAY DIFFRACTIONr_scbond_other1.5961.365375
X-RAY DIFFRACTIONr_scangle_it2.3192.503576
X-RAY DIFFRACTIONr_scangle_other2.3172.504577
X-RAY DIFFRACTIONr_lrange_it5.25918.765566
X-RAY DIFFRACTIONr_lrange_other5.0218.239553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.4550.47590.304204X-RAY DIFFRACTION33.9713
1.455-1.4940.343250.307366X-RAY DIFFRACTION61.8671
1.494-1.5380.26115520X-RAY DIFFRACTION86.7099
1.538-1.5850.268350.258544X-RAY DIFFRACTION97.3109
1.585-1.6370.327260.258556X-RAY DIFFRACTION99.1482
1.637-1.6940.258220.24522X-RAY DIFFRACTION99.6337
1.694-1.7580.3220.225528X-RAY DIFFRACTION100
1.758-1.830.287210.247508X-RAY DIFFRACTION100
1.83-1.9110.289210.235479X-RAY DIFFRACTION100
1.911-2.0040.282260.222454X-RAY DIFFRACTION99.7921
2.004-2.1120.254190.226440X-RAY DIFFRACTION100
2.112-2.2390.271230.201417X-RAY DIFFRACTION100
2.239-2.3930.16923388X-RAY DIFFRACTION100
2.393-2.5840.29150.219366X-RAY DIFFRACTION100
2.584-2.8290.224160.205353X-RAY DIFFRACTION100
2.829-3.160.175130.192300X-RAY DIFFRACTION99.3651
3.16-3.6440.202150.185283X-RAY DIFFRACTION98.6755
3.644-4.4520.145150.18235X-RAY DIFFRACTION100
4.452-6.2470.31190.162198X-RAY DIFFRACTION100
6.247-35.4140.1839119X-RAY DIFFRACTION100

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