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

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Basic information

Entry
Database: PDB / ID: 1icg
TitleSTRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++
Components5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(UFP))-3'
KeywordsDNA/RNA / RNA/DNA HYBRID / FLUORO-URACIL / C-U MISMATCH / G-U MISMATCH / RHODIUM HEXAMMINE / IRIDIUM HEXAMMINE / DNA-RNA COMPLEX
Function / homologyIRIDIUM HEXAMMINE ION / DNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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.B. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O.
History
DepositionMar 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 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)6,3136
Polymers5,6532
Non-polymers6604
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.750, 19.400, 45.840
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H18IrN6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 39.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: cacodylate, iridium hexammine, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2Iridium hexammine11
3MPD11
4MPD12
Crystal grow
*PLUS
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 10, 1998 / Details: Si(III) curvated crystal
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.53→10 Å / Num. all: 6772 / Num. obs: 6518 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 6.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.046 / Net I/σ(I): 25
Reflection shellResolution: 1.53→1.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.4 / Num. unique all: 729 / Rsym value: 0.167 / % possible all: 75
Reflection
*PLUS
Num. measured all: 42723

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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: 1.53→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4
Stereochemistry target values: LOCAL DICTIONARY FROM SMALL MOLECULE STRUCTURES
Details: the two iridium and the two chlorine atoms were refined anisotropically
RfactorNum. reflection% reflectionSelection details
Rfree0.205 562 -RANDOM
Rwork0.177 ---
all0.18 6772 --
obs0.177 6518 96.2 %-
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 1.53→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 370 18 49 437
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_from_restr_planes0.027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.53-1.60.291510.235X-RAY DIFFRACTION0.0275.3
1.6-1.80.2911520.235X-RAY DIFFRACTION0.0288.2
1.8-20.291890.235X-RAY DIFFRACTION0.0295.1
2-40.2912330.235X-RAY DIFFRACTION0.0297.5
4-100.291370.235X-RAY DIFFRACTION0.0296.4
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor all: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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