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- PDB-4u3o: Octameric RNA duplex soaked in manganese(II)chloride -

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Basic information

Entry
Database: PDB / ID: 4u3o
TitleOctameric RNA duplex soaked in manganese(II)chloride
ComponentsRNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3')
KeywordsRNA / duplex / di- and trivalent metal ions
Function / homology: / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,2736
Polymers5,0532
Non-polymers2204
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-16 kcal/mol
Surface area3130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.328, 46.328, 58.075
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
11A-212-

HOH

21B-206-

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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.37 Å3/Da / Density % sol: 48.18 % / Description: Needle-shaped
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: 1.37 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37 Å / Relative weight: 1
ReflectionResolution: 1.8→23.16 Å / Num. all: 78748 / Num. obs: 4140 / % possible obs: 95.74 % / Redundancy: 19 % / Rmerge(I) obs: 0.05784 / Net I/σ(I): 43.26
Reflection shellResolution: 1.8→1.843 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.2178 / Mean I/σ(I) obs: 12.06 / % possible all: 79.91

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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: 4U3L

4u3l


Resolution: 1.8→23.16 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1754 430 10.39 %
Rwork0.1642 --
obs0.1654 4230 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→23.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 4 65 403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005372
X-RAY DIFFRACTIONf_angle_d0.913576
X-RAY DIFFRACTIONf_dihedral_angle_d5.478184
X-RAY DIFFRACTIONf_chiral_restr0.02978
X-RAY DIFFRACTIONf_plane_restr0.00616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-2.06050.21081360.1671162X-RAY DIFFRACTION89
2.0605-2.59540.23251500.19361260X-RAY DIFFRACTION99
2.5954-23.16570.14571440.15181286X-RAY DIFFRACTION100

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