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- PDB-3nd3: Uhelix 16-mer dsRNA -

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Basic information

Entry
Database: PDB / ID: 3nd3
TitleUhelix 16-mer dsRNA
Components5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*UP*UP*UP*UP*UP*UP*U)-3'
KeywordsRNA / double-stranded RNA / U-helix / oligo-U tail / polyU RNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å
AuthorsMooers, B.H. / Singh, A.
CitationJournal: Rna / Year: 2011
Title: The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate.
Authors: Mooers, B.H. / Singh, A.
History
DepositionJun 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,1483
Polymers5,0861
Non-polymers622
Water1,42379
1
A: 5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*UP*UP*UP*UP*UP*UP*U)-3'
hetero molecules

A: 5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*UP*UP*UP*UP*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2966
Polymers10,1722
Non-polymers1244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1670 Å2
ΔGint-28 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.735, 42.735, 126.358
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-17-

K

21A-27-

HOH

31A-28-

HOH

41A-66-

HOH

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Components

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


Mass: 5086.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM NaCacodylate pH 6.0, 10 mM MgCl2, and 1 M LiSO4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.37→18.309 Å / Num. all: 9679 / Num. obs: 9679 / % possible obs: 99.8 % / Redundancy: 17.2 % / Rsym value: 0.026 / Net I/σ(I): 52
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.37-1.4413.10.5031.61782913660.50399.1
1.44-1.5314.60.26131933113250.261100
1.53-1.6414.60.116.81793912320.11100
1.64-1.7714.60.05411.81689411560.054100
1.77-1.9414.70.04615.71588810820.046100
1.94-2.1717.20.03816.8166249690.038100
2.17-2.526.40.03517.3230048710.035100
2.5-3.06260.02618.7193737450.026100
3.06-4.3322.60.02121.3133325890.021100
4.33-19.0617.30.01926.259653440.01998.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→18.309 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.82 / SU ML: 0.14 / σ(F): 0.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 958 9.94 %
Rwork0.182 --
obs0.187 9641 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.297 Å2 / ksol: 0.448 e/Å3
Displacement parametersBiso max: 61.85 Å2 / Biso mean: 34.966 Å2 / Biso min: 19.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.37→18.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 336 2 79 417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019383
X-RAY DIFFRACTIONf_angle_d1.33591
X-RAY DIFFRACTIONf_chiral_restr0.06379
X-RAY DIFFRACTIONf_plane_restr0.0216
X-RAY DIFFRACTIONf_dihedral_angle_d12.579188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.37-1.4430.2681280.2321218134699
1.443-1.5330.2741360.20212151351100
1.533-1.6510.1991350.1681216135199
1.651-1.8170.2551350.1691216135199
1.817-2.080.2511380.18312411379100
2.08-2.6190.2291410.18312601401100
2.619-18.3110.2171450.1781317146299

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