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- PDB-7y8p: Crystal structure of 4'-selenoRNA duplex -

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Basic information

Entry
Database: PDB / ID: 7y8p
TitleCrystal structure of 4'-selenoRNA duplex
ComponentsRNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3')
KeywordsRNA / selen
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKondo, J. / Minakawa, N. / Ohta, M. / Takahashi, H. / Tarashima, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H02108 Japan
CitationJournal: Bioorg.Med.Chem. / Year: 2022
Title: Synthesis and properties of fully-modified 4'-selenoRNA, an endonuclease-resistant RNA analog.
Authors: Ota, M. / Takahashi, H. / Nogi, Y. / Kagotani, Y. / Saito-Tarashima, N. / Kondo, J. / Minakawa, N.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5165
Polymers8,0322
Non-polymers4833
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area4700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.951, 38.107, 31.882
Angle α, β, γ (deg.)90.000, 113.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*(IKS)P*(ILK)P*(IKS)P*GP*AP*GP*UP*CP*C)-3')


Mass: 4016.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


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


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.87 Å3/Da / Density % sol: 34.21 %
Description: The entry contains friedel pairs in F_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, sodium cacodylate, hexammine cobalt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.5→29.25 Å / Num. obs: 18427 / % possible obs: 98.5 % / Redundancy: 3.369 % / Biso Wilson estimate: 17.367 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.095 / Χ2: 1.105 / Net I/σ(I): 11.18 / Num. measured all: 62087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.3170.2814.244352135513120.9460.33696.8
1.54-1.583.4090.2484.974613136813530.9660.29598.9
1.58-1.633.390.1866.144316128212730.9880.22199.3
1.63-1.683.3170.176.884269129912870.9820.20499.1
1.68-1.733.3650.1527.914078123312120.9850.18198.3
1.73-1.793.260.1428.293948121812110.980.16999.4
1.79-1.863.2390.1269.423634113111220.9730.15199.2
1.86-1.943.2070.12210.273537112411030.9770.14798.1
1.94-2.023.1190.10610.953253105810430.9810.12998.6
2.02-2.122.9050.111.132905103110000.9790.12397
2.12-2.233.3840.11813.0732459679590.9810.1499.2
2.23-2.373.1920.08614.0528128878810.9880.10499.3
2.37-2.533.6710.08415.7431318588530.9910.09899.4
2.53-2.743.7340.0817.229578117920.9910.09497.7
2.74-33.7380.06318.6126957407210.9950.07497.4
3-3.353.6630.06519.824146656590.990.07699.1
3.35-3.873.660.05620.1821636025910.9970.06598.2
3.87-4.743.6930.05321.3417544804750.9940.06399
4.74-6.73.5950.05221.5713663853800.9950.06298.7
6.7-29.253.2250.05321.166452112000.9940.06494.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ay2

5ay2


Resolution: 1.5→29.25 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 20.95 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.1986 1827 9.94 %
Rwork0.1596 16556 -
obs0.1634 18383 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.26 Å2 / Biso mean: 13.9295 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.5→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 506 28 124 658
Biso mean--18.28 21.35 -
Num. residues----24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.24991350.22951203133895
1.54-1.580.30991420.20911326146899
1.58-1.640.24221360.18651239137599
1.64-1.690.2871480.18681289143799
1.69-1.760.22361470.1851253140099
1.76-1.840.23971490.19591289143899
1.84-1.940.21081370.18621308144599
1.94-2.060.19611420.16031255139798
2.06-2.220.17411360.16341277141399
2.22-2.440.18391460.152312891435100
2.44-2.80.19891390.15731266140599
2.8-3.520.20031400.13081275141598
3.52-29.250.13471300.12481287141798

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