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- PDB-5tdj: RNA decamer duplex with four 2'-5'-linkages -

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Basic information

Entry
Database: PDB / ID: 5tdj
TitleRNA decamer duplex with four 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: 1.5 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 1.2Sep 6, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_validate_polymer_linkage / Item: _diffrn_detector.detector
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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(*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)6,5023
Polymers6,4142
Non-polymers881
Water79344
1
A: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')

A: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,4142
Polymers6,4142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1080 Å2
ΔGint-4 kcal/mol
Surface area3850 Å2
MethodPISA
2
B: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
hetero molecules

B: RNA (5'-R(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5894
Polymers6,4142
Non-polymers1752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1090 Å2
ΔGint-3 kcal/mol
Surface area3830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.538, 94.455, 21.283
Angle α, β, γ (deg.)90.00, 111.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-101-

SR

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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.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% MPD (2-methyl-2,4-pentanediol), 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetrahydrochloride, 40mM LiCl, 20 mM MgCl2 and 80 mM SrCl2

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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: 1.5→30 Å / Num. obs: 7870 / % possible obs: 96.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.649 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MS9

4ms9


Resolution: 1.5→19.9 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 3.67 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17033 777 9.9 %RANDOM
Rwork0.15207 ---
obs0.15385 7093 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0 Å2-0.39 Å2
2--0.76 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.5→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 424 1 44 469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011468
X-RAY DIFFRACTIONr_bond_other_d0.0130.02202
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.255718
X-RAY DIFFRACTIONr_angle_other_deg1.8233482
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_restr0.110.280
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02246
X-RAY DIFFRACTIONr_gen_planes_other0.010.02116
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_it8.3626.871466
X-RAY DIFFRACTIONr_scbond_other8.3596.872466
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.46513.116717
X-RAY DIFFRACTIONr_long_range_B_refined8.57730.115702
X-RAY DIFFRACTIONr_long_range_B_other8.67330.147699
X-RAY DIFFRACTIONr_rigid_bond_restr4.3273668
X-RAY DIFFRACTIONr_sphericity_free27.524517
X-RAY DIFFRACTIONr_sphericity_bonded24.5425654
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 41 -
Rwork0.262 501 -
obs--88.13 %

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