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- PDB-1idw: STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF ... -

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Basic information

Entry
Database: PDB / ID: 1idw
TitleSTRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[CL]U IN PRESENCE OF RH(NH3)6+++
Components5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
KeywordsDNA/RNA / RNA/DNA HYBRID / RHODIUM HEXAMMINE / C-U MISMATCH / G-U MISMATCH / DNA-RNA COMPLEX
Function / homologyRHODIUM HEXAMINE ION / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsCruse, W. / Saludjian, P. / Neuman, A. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues
Authors: Cruse, W. / Saludjian, P. / Neuman, A. / Prange, T.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of a Mispaired RNA Double Helix at 1.6 A Resolution and Implications for the Prediction of RNA Secondary Structure
Authors: Cruse, W. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O.
History
DepositionApr 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 9, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
B: 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1676
Polymers5,6862
Non-polymers4814
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.820, 19.380, 50.300
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second strand of the dimer is not symmetric

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Components

#1: DNA/RNA hybrid 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UCL))-3'


Mass: 2843.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phosphoramidite method
#2: Chemical ChemComp-RHD / RHODIUM HEXAMINE ION


Mass: 205.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H18N6Rh
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 43.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: cacodylate buffer, MPD, Rhodium-hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate buffer11
2MPD11
3rhodium-hexammine11
4MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.05 Mlithium cacodylate1drop
45 %1drop
535-40 %MPD1reservoir
2RNA/DNA hybrid1drop0.1mg
3rhodium/iridium hexammine1drop0.1mg

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 20, 1997 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→6 Å / Num. all: 3738 / Num. obs: 3641 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.041 / Net I/σ(I): 18
Reflection shellResolution: 1.8→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3 / Num. unique all: 517 / Rsym value: 0.206 / % possible all: 43.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / % possible obs: 85 % / Num. measured all: 13027

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Processing

Software
NameVersionClassification
MADNESSdata collection
ROTAVATAdata reduction
AMoREphasing
SHELXL-97refinement
MADNESSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 165D

165d


Resolution: 1.8→6 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4
Stereochemistry target values: personal dictionary from small molecules
Details: Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. ...Details: Chloro-uracil 9 B disordered at the C2 position. Refined as two-component 1:1 static orientations paired to their symmetry-related mates. The two rhodium atoms are refined anisotropically. One chlorine atom is disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 311 -RANDOM
Rwork0.172 ---
all0.176 3738 --
obs0.172 3641 95 %-
Displacement parametersBiso mean: 18.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 389 20 46 455
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_from_restr_planes0.071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.8-20.21400.169X-RAY DIFFRACTION0.0243.2
2-2.30.191930.164X-RAY DIFFRACTION0.0298.5
2.3-2.70.211800.176X-RAY DIFFRACTION0.0298.7
2.7-3.50.187690.168X-RAY DIFFRACTION0.0296.8
3.5-60.19300.195X-RAY DIFFRACTION0.0276.5
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.071
X-RAY DIFFRACTIONs_chiral_restr0.097

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