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- PDB-5tko: RNA heptamer duplex with one 2'-5'-linkage -

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Basic information

Entry
Database: PDB / ID: 5tko
TitleRNA heptamer duplex with one 2'-5'-linkage
Components
  • RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')
  • RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
KeywordsRNA / 2'-5'-LINKAGE
Function / homology: / RNA
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsLuo, Z. / Sheng, J.
CitationJournal: To Be Published
Title: RNA heptamer duplex with one 2'-5'-linkage
Authors: Luo, Z. / Sheng, J. / Wang, R.
History
DepositionOct 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')
C: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8945
Polymers8,8364
Non-polymers591
Water1,56787
1
A: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4773
Polymers4,4182
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-5 kcal/mol
Surface area2800 Å2
MethodPISA
2
C: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3')
D: RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')


Theoretical massNumber of molelcules
Total (without water)4,4182
Polymers4,4182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-9 kcal/mol
Surface area2870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.541, 52.941, 27.732
Angle α, β, γ (deg.)90.00, 95.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 2157.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: RNA chain RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3')


Mass: 2260.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Precipitant: 40 mM sodium cacodylate pH5.5, 10% (v/v) MPD, 20 mM hexamine cobalt (III) chloride, 20mM MgCl2 Reservoir: 35% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→30 Å / Num. obs: 11869 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.8
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.95 / % possible all: 100

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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: 4U37

4u37


Resolution: 1.52→27.58 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.904 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.075 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17727 1115 10.2 %RANDOM
Rwork0.14412 ---
obs0.14744 9775 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.635 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å2-0 Å20.07 Å2
2---1.05 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 1.52→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 584 1 87 672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011648
X-RAY DIFFRACTIONr_bond_other_d0.0060.02278
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.27998
X-RAY DIFFRACTIONr_angle_other_deg3.8413670
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_restr0.0910.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02328
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02146
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_it3.2743.198648
X-RAY DIFFRACTIONr_scbond_other3.2753.199649
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8436.075999
X-RAY DIFFRACTIONr_long_range_B_refined4.33714.444953
X-RAY DIFFRACTIONr_long_range_B_other4.30314.408951
X-RAY DIFFRACTIONr_rigid_bond_restr4.4383926
X-RAY DIFFRACTIONr_sphericity_free26.713536
X-RAY DIFFRACTIONr_sphericity_bonded11.9885914
LS refinement shellResolution: 1.516→1.598 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.172 105 -
Rwork0.163 820 -
obs--53.97 %

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