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- PDB-4u3p: Octameric RNA duplex co-crystallized with strontium(II)chloride -

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Basic information

Entry
Database: PDB / ID: 4u3p
TitleOctameric RNA duplex co-crystallized with strontium(II)chloride
ComponentsRNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-3')
KeywordsRNA / duplex / di- and trivalent metal ions
Function / homologySTRONTIUM ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.866 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 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)5,2284
Polymers5,0532
Non-polymers1752
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-54 kcal/mol
Surface area3030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.480, 45.480, 57.980
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-102-

SR

21A-111-

HOH

31A-113-

HOH

41A-116-

HOH

51B-204-

HOH

61B-207-

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-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 8000, 0.2 M strontium chloride, 0.2 M ammonium acetate, 0.01 M magnesium acetate, 0.05 M sodium cacodylate buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.6 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6 Å / Relative weight: 1
ReflectionResolution: 1.866→32.58 Å / Num. obs: 3728 / % possible obs: 99.79 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.03566 / Net I/σ(I): 34.84
Reflection shellResolution: 1.866→1.932 Å / Redundancy: 7 % / Rmerge(I) obs: 0.4714 / Mean I/σ(I) obs: 4.06 / % possible all: 97.96

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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: 1.866→32.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 760 10.24 %
Rwork0.1799 --
obs0.1852 3719 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.866→32.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 2 74 410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004372
X-RAY DIFFRACTIONf_angle_d0.776576
X-RAY DIFFRACTIONf_dihedral_angle_d7.647184
X-RAY DIFFRACTIONf_chiral_restr0.03278
X-RAY DIFFRACTIONf_plane_restr0.00616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8662-2.01030.30831580.23411316X-RAY DIFFRACTION98
2.0103-2.21260.29571460.21141334X-RAY DIFFRACTION99
2.2126-2.53260.30111620.2081344X-RAY DIFFRACTION100
2.5326-3.19040.25471380.19671328X-RAY DIFFRACTION100
3.1904-32.58530.1851560.15191338X-RAY DIFFRACTION99

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