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- PDB-4u47: Octameric RNA duplex soaked in terbium(III)chloride -

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Basic information

Entry
Database: PDB / ID: 4u47
TitleOctameric RNA duplex soaked in terbium(III)chloride
ComponentsRNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3')
KeywordsRNA / duplex / di- and trivalent metal ions
Function / homologyTERBIUM(III) ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å
AuthorsSchaffer, M.F. / Spingler, B. / Schnabl, J. / Peng, G. / Olieric, V. / Sigel, R.K.O.
CitationJournal: Int J Mol Sci / Year: 2016
Title: The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations.
Authors: Schaffer, M.F. / Peng, G. / Spingler, B. / Schnabl, J. / Wang, M. / Olieric, V. / Sigel, R.K.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Dec 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,3714
Polymers5,0532
Non-polymers3182
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-21 kcal/mol
Surface area3000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.506, 46.506, 56.627
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-105-

HOH

21B-107-

HOH

31A-201-

HOH

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Components

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


Mass: 2526.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Tb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 400, 0.2 M calcium chloride, 0.002 M spermine, 0.05 M hepes sodium buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.64 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.64 Å / Relative weight: 1
ReflectionResolution: 1.952→32.82 Å / Num. obs: 3225 / % possible obs: 96.82 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.04999 / Net I/σ(I): 33.19
Reflection shellResolution: 1.952→2.02 Å / Redundancy: 9 % / Rmerge(I) obs: 0.4356 / Mean I/σ(I) obs: 5.35 / % possible all: 89.57

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4U3L

4u3l


Resolution: 1.952→32.82 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 329 10.2 %
Rwork0.172 --
obs0.1755 3224 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 2 37 373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004372
X-RAY DIFFRACTIONf_angle_d0.783576
X-RAY DIFFRACTIONf_dihedral_angle_d5.437184
X-RAY DIFFRACTIONf_chiral_restr0.02678
X-RAY DIFFRACTIONf_plane_restr0.00516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9517-2.45880.33091640.24781414X-RAY DIFFRACTION94
2.4588-32.82530.18141650.1561481X-RAY DIFFRACTION99

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