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Basic information

Entry
Database: PDB / ID: 7edu
TitleRNA duplex containing C-Au-C base pair
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
KeywordsRNA / Metal-mediated base pair / Gold
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKondo, J. / Iwase, E.
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-Au-C base pair
Authors: Kondo, J. / Iwase, E.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,9378
Polymers15,1494
Non-polymers7884
Water27015
1
A: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9694
Polymers7,5752
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-19 kcal/mol
Surface area4320 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9694
Polymers7,5752
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-19 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.216, 29.216, 257.794
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 3787.312 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium cacodylate, MPD, spermine tetrahydrochloride, ammonium chloride, gold chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.03906 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03906 Å / Relative weight: 1
ReflectionResolution: 2.3→25.18 Å / Num. obs: 10301 / % possible obs: 94.1 % / Redundancy: 2.58 % / Biso Wilson estimate: 48.631 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.073 / Χ2: 3.113 / Net I/σ(I): 11.1 / Num. measured all: 26576
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
2.3-2.362.6380.3162.7319477897380.8850.39493.5
2.36-2.422.630.272.9122098588400.9310.33797.9
2.42-2.492.7060.2353.8219327337140.9270.29197.4
2.49-2.572.5840.1984.518637397210.950.24597.6
2.57-2.652.4860.1595.4418897907600.9570.20196.2
2.65-2.752.5980.1227.5815466125950.9720.15397.2
2.75-2.852.6160.1328.0218007056880.9550.16797.6
2.85-2.972.7080.09711.217416636430.9730.12197
2.97-3.12.6340.07513.614965925680.9840.09495.9
3.1-3.252.5820.06515.3114516195620.9860.08390.8
3.25-3.432.5790.06117.0412485244840.9850.07892.4
3.43-3.632.480.05617.3112705895120.990.07186.9
3.63-3.892.3620.05117.729594674060.9920.06686.9
3.89-4.22.3290.04718.7410344944440.990.06189.9
4.2-4.62.5790.04719.989263973590.990.0690.4
4.6-5.142.5670.04520.189243943600.9930.05791.4
5.14-5.942.5170.04420.038183543250.9950.05591.8
5.94-7.272.4680.03720.656492972630.9950.04788.6
7.27-10.282.6750.0321.955592162090.9970.03896.8
10.28-25.182.8640.0224.033151171100.9990.02494

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RNA duplex constructed using Coot

Resolution: 2.3→25.18 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1037 10.08 %
Rwork0.1766 9255 -
obs0.1819 10292 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.12 Å2 / Biso mean: 35.81 Å2 / Biso min: 22.45 Å2
Refinement stepCycle: final / Resolution: 2.3→25.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1000 4 15 1019
Biso mean--45.39 32.96 -
Num. residues----48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.420.38861580.28621357151594
2.42-2.570.31521510.24451343149497
2.57-2.770.29561540.24991355150997
2.77-3.050.29831530.23211342149597
3.05-3.490.24541550.2011284143992
3.49-4.390.22351220.15261271139389
4.39-25.180.1271440.10471303144791

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