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- PDB-7ecj: RNA duplex containing C-A base pairs -

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Basic information

Entry
Database: PDB / ID: 7ecj
TitleRNA duplex containing C-A base pairs
ComponentsDNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
KeywordsRNA / mismatch
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKondo, J. / Uchida, 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 C-A base pairs
Authors: Kondo, J. / Uchida, Y.
History
DepositionMar 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
B: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
C: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,6233
Polymers11,6233
Non-polymers00
Water00
1
A: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')
B: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7482
Polymers7,7482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint3 kcal/mol
Surface area4220 Å2
MethodPISA
2
C: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')

C: DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7482
Polymers7,7482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2150 Å2
ΔGint2 kcal/mol
Surface area4370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.780, 47.780, 186.215
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: RNA chain DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))-R(P*GP*AP*AP*UP*CP*C)-3')


Mass: 3874.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, sodium cacodylate, spermine tetrahydrochloride, lithium nitrate

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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: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→46.55 Å / Num. obs: 2674 / % possible obs: 99.7 % / Redundancy: 8.588 % / Biso Wilson estimate: 66.095 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.075 / Χ2: 0.897 / Net I/σ(I): 21.51 / Num. measured all: 22964
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
3.1-3.189.4750.4155.1419142042020.9930.43999
3.18-3.279.380.2297.715571661660.9960.242100
3.27-3.379.3220.2647.6216501771770.9950.279100
3.37-3.478.8840.2747.3916081811810.9950.291100
3.47-3.589.080.19610.1614801631630.9980.208100
3.58-3.719.1280.18511.0714971641640.9980.196100
3.71-3.858.1660.12312.6212821571570.9980.131100
3.85-4.018.0120.10215.6413061631630.9980.109100
4.01-4.189.0280.09820.2412911431430.9980.104100
4.18-4.399.3660.09123.4213301431420.9950.09699.3
4.39-4.638.5520.05729.9711461351340.9990.06199.3
4.63-4.918.4780.05829.2711361351340.9980.06299.3
4.91-5.257.9130.05332.419971271260.9980.05699.2
5.25-5.678.4040.04239.589161091090.9990.045100
5.67-6.218.5740.04536.919861151150.9990.048100
6.21-6.948.4380.04437.638861051050.9990.046100
6.94-8.017.7420.03644.6475197970.9990.038100
8.01-9.817.5130.03448.24586787810.036100
9.81-13.886.0830.02650.4343872720.9990.029100
13.88-46.554.50.0344.6320747460.9990.03497.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→46.55 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 263 9.95 %
Rwork0.2311 2379 -
obs0.2364 2642 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.07 Å2 / Biso mean: 73.9224 Å2 / Biso min: 32.02 Å2
Refinement stepCycle: final / Resolution: 3.1→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 756 0 0 756
Num. residues----36
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.910.34121230.27451119124297
3.91-46.550.26491400.216512601400100

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