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- PDB-5ay3: Crystal structure of RNA duplex containing C-C base pairs -

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Basic information

Entry
Database: PDB / ID: 5ay3
TitleCrystal structure of RNA duplex containing C-C base pairs
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')
KeywordsRNA / X-Ray analysis / metallo base pair / Ag(I)
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsKondo, J. / Tada, Y. / Dairaku, T. / Saneyoshi, H. / Okamoto, I. / Tanaka, Y. / Ono, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Authors: Kondo, J. / Tada, Y. / Dairaku, T. / Saneyoshi, H. / Okamoto, I. / Tanaka, Y. / Ono, A.
History
DepositionAug 6, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / reflns_shell
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*(CBR)P*GP*A*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7002
Polymers7,7002
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-0 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.160, 44.460, 27.370
Angle α, β, γ (deg.)90.00, 109.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3850.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD, Spermine, Lithium Nitrate, MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
1.41.44179410.243
1.441.48165510.192
1.481.52169410.151
1.521.57159410.12
1.571.62157310.093
1.621.67154410.063
1.671.74143010.053
1.741.81145710.052
1.811.89130010.044
1.891.98132210.04
1.982.09126410.036
2.092.22111710.034
2.222.37109210.032
2.372.5699310.03
2.562.892710.028
2.83.1384610.022
3.133.6272310.022
3.624.4363210.02
4.436.2750110.023
6.2725.825410.021
ReflectionResolution: 1.2→25.8 Å / Num. obs: 19127 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 17.18 Å2 / Net I/σ(I): 22.16
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.2-1.2330.9620.1885.414234142714050.22798.5
1.23-1.270.9750.1616.64274136213550.19499.5
1.27-1.30.9780.1527.014478138413740.18299.3
1.3-1.340.9810.1298.384231128612850.15499.9
1.34-1.390.9860.119.523986125612480.13399.4
1.39-1.440.9910.08711.934074125512470.10499.4
1.44-1.490.9930.07214.253800117211650.08699.4
1.49-1.550.9950.05717.343641110410990.06899.5
1.55-1.620.9970.04820.423470108810900.057100
1.62-1.70.9990.03526.163595107410620.04198.9
1.7-1.790.9980.03229.7331119759730.03999.8
1.79-1.90.9980.03132.5732449539490.03799.6
1.9-2.030.9980.02736.1428858798750.03399.5
2.03-2.190.9990.02738.8527238258180.03299.2
2.19-2.40.9990.02541.4724197577480.0398.8
2.4-2.690.9990.02345.3323106986850.02798.1
2.69-3.10.9990.0248.4619616196110.02598.7
3.1-3.80.9990.01852.4116835105040.02298.8
3.8-5.370.9990.01953.1913224084040.02299
5.37-25.80.9980.0250.647182352300.02497.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
CNS1.3refinement
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.2→25.8 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.1985 1891 9.8 %
Rwork0.1841 17236 -
obs-19127 99.2 %
Solvent computationBsol: 43.3617 Å2
Displacement parametersBiso max: 60.77 Å2 / Biso mean: 16.3542 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.417 Å20 Å2-2.148 Å2
2---1.415 Å20 Å2
3---1.833 Å2
Refinement stepCycle: LAST / Resolution: 1.2→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 500 40 171 711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.1192
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it1.5462.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.240.27291900.24871682187296.3
1.24-1.290.27421750.24881717189299.6
1.29-1.350.27791790.25041733191299.7
1.35-1.420.25652110.22861686189799.6
1.42-1.510.21682130.20921714192799.5
1.51-1.630.20741840.18921738192299.8
1.63-1.790.19911560.17591749190599.7
1.79-2.050.19951660.17681747191399.7
2.05-2.590.20612250.19371703192899
2.59-1000.16061920.15591767195999.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1bru.param
X-RAY DIFFRACTION2dna-rna_free.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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