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- PDB-5ay4: Crystal structure of RNA duplex containing C-C base pairs obtaine... -

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Basic information

Entry
Database: PDB / ID: 5ay4
TitleCrystal structure of RNA duplex containing C-C base pairs obtained in the presence of Hg(II)
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')
KeywordsRNA / X-Ray analysis / metallo base pair / Ag(I) / Hg(II)
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

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


Theoretical massNumber of molelcules
Total (without water)7,7233
Polymers7,7002
Non-polymers231
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-10 kcal/mol
Surface area4200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.000, 44.540, 27.550
Angle α, β, γ (deg.)90.000, 109.100, 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*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')


Mass: 3850.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD, Spermine, Sodium 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: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→26 Å / Num. obs: 6831 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.161 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.096 / Χ2: 0.939 / Net I/σ(I): 13.38 / Num. measured all: 45309
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.750.9550.3235.5830675074900.35396.6
1.75-1.790.9570.3175.9131424814780.34599.4
1.79-1.850.9590.296.3432454824860.314100
1.85-1.90.9740.2327.3928704544510.25399.3
1.9-1.960.9810.2128.2431014574570.23100
1.96-2.030.9810.1819.829234384350.19699.3
2.03-2.110.9840.16910.4628254304290.18499.8
2.11-2.20.990.14211.4426433913910.154100
2.2-2.290.990.13112.4827064044000.14299
2.29-2.410.9910.10914.4823253523530.119100
2.41-2.540.9920.10215.725293603600.11100
2.54-2.690.9960.09217.1123423393370.199.4
2.69-2.880.9930.08618.3920343163190.095100
2.88-3.110.9980.06421.7720073002940.0798
3.11-3.40.9990.06223.2918042752740.06799.6
3.4-3.80.9970.06124.6816382402400.066100
3.8-4.390.9980.05825.8714072192180.06399.5
4.39-5.380.9960.06626.1612521891870.07298.9
5.38-7.610.9960.06424.539661501490.06999.3
7.610.9950.05226.0448382810.05698.8

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Processing

Software
NameVersionClassification
CNS1.3refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AY3

5ay3


Resolution: 1.7→26 Å / FOM work R set: 0.8766 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.1956 745 10.9 %
Rwork0.1601 6086 -
obs-6831 99.6 %
Solvent computationBsol: 36.2882 Å2
Displacement parametersBiso max: 58.96 Å2 / Biso mean: 18.972 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.208 Å20 Å2-2.485 Å2
2---1.831 Å20 Å2
3---0.622 Å2
Refinement stepCycle: final / Resolution: 1.7→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 500 1 158 659
Biso mean--22.38 31.88 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.839
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.3932
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it1.8382.5
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 (%)
1.7-1.760.2062700.19558465496.3
1.76-1.830.2388610.2094607668100
1.83-1.910.2662850.2036601686100
1.91-2.020.2653770.2041609686100
2.02-2.140.1992810.1843594675100
2.14-2.310.2374710.1766615686100
2.31-2.540.2001730.1678612685100
2.54-2.910.1889740.1532620694100
2.91-3.660.1732780.138960768599.9
3.66-260.1464750.126363771299.9
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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