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- PDB-1id9: STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF R... -

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Basic information

Entry
Database: PDB / ID: 1id9
TitleSTRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF RH(NH3)6+++
Components5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3'
KeywordsDNA/RNA / RNA/DNA HYBRID / FLUORO URACIL / RHODIUM(III) HEXAMMINE / C-U MISMATCH / G-U mismatch / DNA-RNA COMPLEX
Function / homologyRHODIUM HEXAMINE ION / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 4, 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 1.3Aug 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*(UFP))-3'
B: 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1346
Polymers5,6532
Non-polymers4814
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.730, 19.390, 45.830
Angle α, β, γ (deg.)90.00, 105.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 2826.694 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.: 50 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Cacodylate, MPD, rhodium(iii) hexammine, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cacodylate11
2MPD11
3rhodium(iii) 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: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.967 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 8, 1998 / Details: Si(111)
RadiationMonochromator: curvated Si(111) mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.6→11 Å / Num. all: 4425 / Num. obs: 4339 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 9 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.045 / Net I/σ(I): 21
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 5 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 4.1 / Num. unique all: 786 / Rsym value: 0.16 / % possible all: 76
Reflection
*PLUS
Lowest resolution: 11 Å / % possible obs: 92 % / Redundancy: 9 % / Num. measured all: 38535 / Rmerge(I) obs: 0.057

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 165D

165d


Resolution: 1.6→11 Å
Isotropic thermal model: Isotropic, the rhodium atoms were anisotropically refined
Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4
Stereochemistry target values: personal dictionary from small molecules
Details: Last fluoro-uracil (chain B) refined as a two-position disorder
RfactorNum. reflection% reflectionSelection details
Rfree0.195 410 -RANDOM
Rwork0.156 ---
all0.155 4425 --
obs0.153 4339 98 %-
Refinement stepCycle: LAST / Resolution: 1.6→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 385 19 50 454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.074
X-RAY DIFFRACTIONs_from_restr_planes0.02
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.6-1.70.2640.181X-RAY DIFFRACTION0.0276.9
1.7-1.80.198650.166X-RAY DIFFRACTION0.0274.8
1.8-20.195950.165X-RAY DIFFRACTION0.0277.6
2-30.191350.156X-RAY DIFFRACTION0.0269.1
3-50.2420.117X-RAY DIFFRACTION0.0254.4
5-110.2290.13X-RAY DIFFRACTION0.0242.2
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 11 Å / σ(F): 2 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.02
X-RAY DIFFRACTIONs_chiral_restr0.074

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