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- PDB-7edt: RNA duplex containing CC mispairs -

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Basic information

Entry
Database: PDB / ID: 7edt
TitleRNA duplex containing CC mispairs
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*CP*CP*GP*GP*(5BU)P*CP*C)-3')
KeywordsRNA / Mismatch / base pair
Function / homologySPERMINE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKondo, J. / Tada, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)24245037 Japan
CitationJournal: To Be Published
Title: RNA duplex containing CC mispairs
Authors: Kondo, J. / Tada, Y.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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*CP*UP*CP*CP*GP*GP*(5BU)P*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*CP*CP*GP*GP*(5BU)P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9904
Polymers7,7642
Non-polymers2252
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-16 kcal/mol
Surface area4180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.296, 24.852, 28.249
Angle α, β, γ (deg.)93.850, 106.020, 103.210
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 3882.208 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9204 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9204 Å / Relative weight: 1
ReflectionResolution: 1.2→19.27 Å / Num. obs: 17973 / % possible obs: 93.8 % / Redundancy: 3.85 % / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.079 / Χ2: 0.94 / Net I/σ(I): 10 / Num. measured all: 69661 / Scaling rejects: 524
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2% possible allRejects
1.2-1.243.750.2613.6662117660.8292.3
1.24-1.293.90.2523.8696617860.892.88
1.29-1.353.910.2284.1703517990.7993.5
1.35-1.423.90.1994.6701517960.7393.83
1.42-1.513.880.1665.2704718140.7394.59
1.51-1.633.910.1226.8709618120.7194.913
1.63-1.793.910.09110.1716718230.7595.338
1.79-2.053.860.0714.2720318420.8795.791
2.05-2.583.820.05522.2714118301.2695.9154
2.58-19.273.610.06127.6637017052.1289.1208

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
d*TREK9.4SSIdata scaling
d*TREKdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RNA duplex constructed using Coot

Resolution: 1.2→19.27 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 15.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1767 1840 10.25 %
Rwork0.1439 16109 -
obs0.1471 17949 93.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.9 Å2 / Biso mean: 15.9171 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: final / Resolution: 1.2→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 504 12 163 679
Biso mean--21.65 28.66 -
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 (%)
1.2-1.230.19531530.15491218137192
1.23-1.270.1971420.14161215135792
1.27-1.310.21011450.15761219136493
1.31-1.360.18621370.13721255139294
1.36-1.410.17391330.14291228136193
1.41-1.470.17971500.14441234138495
1.47-1.550.18491380.14111264140294
1.55-1.650.16761270.1271257138495
1.65-1.780.14731580.1221268142696
1.78-1.960.17711560.13911235139195
1.96-2.240.16441400.14081268140895
2.24-2.820.19221310.16111296142797
2.82-19.270.1761300.14781152128287

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