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- PDB-3nd4: Watson-Crick 16-mer dsRNA -

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Basic information

Entry
Database: PDB / ID: 3nd4
TitleWatson-Crick 16-mer dsRNA
Components5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3'
KeywordsRNA / double-stranded RNA / 16 base pair RNA
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.524 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 1.2Feb 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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*CP*UP*UP*CP*UP*CP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1694
Polymers5,0831
Non-polymers863
Water1,71195
1
A: 5'-R(*AP*GP*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*CP*U)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)10,3398
Polymers10,1662
Non-polymers1736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1680 Å2
ΔGint-24 kcal/mol
Surface area5890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.094, 41.094, 123.690
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-

MG

21A-18-

K

31A-24-

HOH

41A-25-

HOH

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Components

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


Mass: 5083.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.98 Å3/Da / Density % sol: 37.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 mM MgCl2, 10 mM Spermine, 2M lithium sulfate, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: Varimax-HF confocal optical system
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.524→18.39 Å / Num. all: 6419 / Num. obs: 6419 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rsym value: 0.041 / Net I/σ(I): 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.52-1.614.60.1584.740638810.15897.1
1.61-1.77.60.104766728820.104100
1.7-1.827.70.0759.663378200.075100
1.82-1.977.80.0691059747670.069100
1.97-2.167.90.05412.257807280.054100
2.16-2.417.90.04613.450976460.046100
2.41-2.787.80.04114.844865720.041100
2.78-3.417.60.03513.637734960.035100
3.41-4.827.50.0341429523920.03499.9
4.82-18.397.10.03314.316592350.03398.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.524→18.39 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.859 / SU ML: 0.18 / σ(F): 1.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 642 10.01 %
Rwork0.172 --
obs0.176 6412 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.549 Å2 / ksol: 0.462 e/Å3
Displacement parametersBiso max: 47.19 Å2 / Biso mean: 17.26 Å2 / Biso min: 6.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å2-0 Å2-0 Å2
2--0.031 Å20 Å2
3----0.062 Å2
Refinement stepCycle: LAST / Resolution: 1.524→18.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 336 3 95 434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018383
X-RAY DIFFRACTIONf_angle_d1.614591
X-RAY DIFFRACTIONf_chiral_restr0.07479
X-RAY DIFFRACTIONf_plane_restr0.02116
X-RAY DIFFRACTIONf_dihedral_angle_d12.291188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.524-1.6420.2341230.1821108123198
1.642-1.8070.2281260.17311251251100
1.807-2.0680.2451290.17511611290100
2.068-2.6040.2371270.17611541281100
2.604-18.3910.1831370.16412221359100

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