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- PDB-8tdz: 16mer self-complementary duplex RNA with D:U pair sequence 2 -

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Basic information

Entry
Database: PDB / ID: 8tdz
Title16mer self-complementary duplex RNA with D:U pair sequence 2
ComponentsRNA
KeywordsRNA / Diaminopurine / Non-canonical base pair
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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

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Assembly

Deposited unit
A: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2592
Polymers5,0981
Non-polymers1611
Water1,24369
1
A: RNA
hetero molecules

A: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5184
Polymers10,1962
Non-polymers3222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3030 Å2
ΔGint-6 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.870, 41.870, 124.300
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

21A-240-

HOH

31A-249-

HOH

41A-261-

HOH

51A-265-

HOH

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Components

#1: RNA chain RNA


Mass: 5098.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CoH18N6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 41.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40 mM Lithium chloride, 20 mM Magnesium chloride hexahydrate, 40 mM Sodium cacodylate trihydrate pH 5.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 2 mM Hexammine cobalt(III) 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: 1.038413 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038413 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 5403 / % possible obs: 99.6 % / Redundancy: 8.7 % / Biso Wilson estimate: 7.47 Å2 / CC star: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.019 / Rrim(I) all: 0.057 / Χ2: 0.865 / Net I/σ(I): 35.5
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 5 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 250 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.084 / Rrim(I) all: 0.204 / Χ2: 1.059 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→41.43 Å / SU ML: 0.1523 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 17.5942
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 262 5.29 %
Rwork0.1882 4691 -
obs0.19 4953 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.3 Å2
Refinement stepCycle: LAST / Resolution: 1.64→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 337 7 69 413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047382
X-RAY DIFFRACTIONf_angle_d1.0025599
X-RAY DIFFRACTIONf_chiral_restr0.038778
X-RAY DIFFRACTIONf_plane_restr0.00816
X-RAY DIFFRACTIONf_dihedral_angle_d5.3396180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.64-1.70.2029150.195124526050
1.7-1.770.2847130.186536237571
1.77-1.850.1908280.196647049893
1.85-1.940.2434300.2001497527100
1.95-2.070.2821250.2134512537100
2.07-2.230.224370.1946499536100
2.23-2.450.2327290.2115519548100
2.45-2.80.2842290.2129513542100
2.81-3.530.1844300.174950753797
3.53-41.430.1778260.156956759399

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