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- PDB-8yno: RNA duplex containing Formamide -

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Basic information

Entry
Database: PDB / ID: 8yno
TitleRNA duplex containing Formamide
ComponentsRNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHU)P*CP*C)-3')
KeywordsRNA / Formamide
Function / homologySPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsKondo, J. / Abe, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR18S1 Japan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs.
Authors: Nomura, K. / An, S. / Kobayashi, Y. / Kondo, J. / Shi, T. / Murase, H. / Nakamoto, K. / Kimura, Y. / Abe, N. / Ui-Tei, K. / Abe, H.
History
DepositionMar 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,0693
Polymers7,8672
Non-polymers2021
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint0 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.633, 43.063, 28.043
Angle α, β, γ (deg.)90.000, 109.510, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*CP*(5BU)P*CP*GP*AP*GP*(HHU)P*CP*C)-3')


Mass: 3933.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: MPD, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.91962 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91962 Å / Relative weight: 1
ReflectionResolution: 1.3→26.43 Å / Num. obs: 15146 / % possible obs: 98.3 % / Redundancy: 6.449 % / Biso Wilson estimate: 16.777 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.064 / Χ2: 0.985 / Net I/σ(I): 19.46 / Num. measured all: 97678
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.335.1210.1469.519680.9820.16384.2
1.33-1.376.1410.13711.1810700.990.1598.4
1.37-1.416.8030.1271310790.9910.13899.7
1.41-1.456.9540.11414.3310510.9930.12399.9
1.45-1.56.8660.10315.839860.9940.11299.6
1.5-1.556.7380.09816.399880.9950.10799.2
1.55-1.616.5660.08618.539410.9970.09499.9
1.61-1.686.1120.07719.278930.9960.08498.9
1.68-1.756.8570.07221.778800.9970.078100
1.75-1.846.8070.07122.988340.9960.07799.4
1.84-1.946.6690.06523.67730.9970.071100
1.94-2.056.5930.06524.577690.9960.0799.2
2.05-2.26.3470.0625.116980.9960.06599.6
2.2-2.375.7820.06224.146460.9950.06898.9
2.37-2.66.6180.05526.346100.9980.0699
2.6-2.96.6190.05827.265480.9980.063100
2.9-3.356.4340.05727.644950.9980.06299
3.35-4.116.0960.04927.254160.9980.05398.1
4.11-5.815.9250.04426.953200.9980.04899.4
5.81-26.435.8290.05526.551810.9970.0698.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→26.43 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1727 1502 9.92 %
Rwork0.1507 13635 -
obs0.1529 15137 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 37.37 Å2 / Biso mean: 12.5496 Å2 / Biso min: 6.72 Å2
Refinement stepCycle: final / Resolution: 1.3→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 512 8 170 690
Biso mean--17.01 20.17 -
Num. residues----24
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.340.18261190.17141088120785
1.34-1.390.18371380.166912451383100
1.39-1.440.20191330.158812411374100
1.44-1.510.19521360.154112491385100
1.51-1.590.17761340.151812601394100
1.59-1.690.17271350.13671239137499
1.69-1.820.18081390.136412551394100
1.82-20.17481400.155912791419100
2-2.290.17211410.160512421383100
2.29-2.890.18371430.181212551398100
2.89-26.430.15471440.13041282142699

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