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- PDB-5ay2: Crystal structure of RNA duplex containing C-Ag(I)-C base pairs -

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Basic information

Entry
Database: PDB / ID: 5ay2
TitleCrystal structure of RNA duplex containing C-Ag(I)-C base pairs
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')
KeywordsRNA / metallo base pair / Ag(I)
Function / homologySILVER ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 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 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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*(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')
C: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')
D: 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)15,8328
Polymers15,4014
Non-polymers4314
Water5,909328
1
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)7,9164
Polymers7,7002
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-15 kcal/mol
Surface area4050 Å2
MethodPISA
2
C: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')
D: 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)7,9164
Polymers7,7002
Non-polymers2162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-15 kcal/mol
Surface area4090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.480, 46.860, 89.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ag
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
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
ReflectionResolution: 1.3→45 Å / Num. obs: 31405 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 19.71 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 28.02
Reflection shellResolution: 1.3→1.33 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7.28 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CNS1.3refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→45 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.189 3145 10 %
Rwork0.174 --
obs0.174 31405 99.7 %
Solvent computationBsol: 40.68 Å2
Displacement parametersBiso mean: 20.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.382 Å20 Å20 Å2
2--1.219 Å20 Å2
3----1.601 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1000 4 328 1332
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it1.172
X-RAY DIFFRACTIONc_scangle_it1.6572.5
LS refinement shellResolution: 1.3→1.35 Å
RfactorNum. reflection% reflection
Rfree0.2806 282 -
Rwork0.2435 2756 -
obs--97.9 %
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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