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- PDB-5tdk: RNA decamer duplex with eight 2'-5'-linkages -

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Basic information

Entry
Database: PDB / ID: 5tdk
TitleRNA decamer duplex with eight 2'-5'-linkages
ComponentsRNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
KeywordsRNA / 2'-5'-LINKAGE / PLANT PROTEIN
Function / homologySTRONTIUM ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsLuo, Z. / Sheng, J.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural insights into RNA duplexes with multiple 2 -5 -linkages.
Authors: Shen, F. / Luo, Z. / Liu, H. / Wang, R. / Zhang, S. / Gan, J. / Sheng, J.
History
DepositionSep 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_validate_polymer_linkage
Revision 1.3Jan 16, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Oct 4, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
B: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8527
Polymers6,4142
Non-polymers4385
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-131 kcal/mol
Surface area3830 Å2
Unit cell
Length a, b, c (Å)24.820, 47.020, 42.880
Angle α, β, γ (deg.)90.00, 96.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-104-

SR

21A-201-

HOH

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Components

#1: RNA chain RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')


Mass: 3206.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: CHEMICALLY SYNTHESIZED BY SOLID PHASE SYNTHESIS AND PURIFIED BY HPLC
Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM sodium cacodylate buffer (pH 7.0), 10% (v/v) MPD (2-methyl-2,4-pentanediol), 12 mM spermine tetrahydrochloride, 40 mM LiCl, 80 mM SrCl2 and 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→18.7 Å / Num. obs: 8980 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.3
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MSB

4msb


Resolution: 1.43→18.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.929 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20585 476 5.3 %RANDOM
Rwork0.16781 ---
obs0.16984 8504 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.014 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å21.8 Å2
2---1.79 Å2-0 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.43→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 424 5 66 495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011464
X-RAY DIFFRACTIONr_bond_other_d0.0040.02202
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.256702
X-RAY DIFFRACTIONr_angle_other_deg3.1833482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02246
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02116
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4053.714464
X-RAY DIFFRACTIONr_scbond_other3.4043.715463
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9197.004703
X-RAY DIFFRACTIONr_long_range_B_refined5.10617.4342442
X-RAY DIFFRACTIONr_long_range_B_other5.05117.3682426
X-RAY DIFFRACTIONr_rigid_bond_restr3.8663666
X-RAY DIFFRACTIONr_sphericity_free37.3152
X-RAY DIFFRACTIONr_sphericity_bonded16.3055695
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 31 -
Rwork0.248 596 -
obs--91.67 %

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