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- PDB-1iha: Structure of the Hybrid RNA/DNA R-GCUUCGGC-D[BR]U in Presence of ... -

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Basic information

Entry
Database: PDB / ID: 1iha
TitleStructure of the Hybrid RNA/DNA R-GCUUCGGC-D[BR]U in Presence of RH(NH3)6+++
Components5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(BRU))-3'
KeywordsDNA/RNA / RNA/DNA HYBRID / BROMO URACIL / RHODIUM(III) HEXAMMINE / C-U 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.B. / 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
DepositionApr 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 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 1.4Aug 16, 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*(BRU))-3'
B: 5'-R(*GP*CP*UP*UP*CP*GP*GP*C)-D(P*(BRU))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2566
Polymers5,7752
Non-polymers4814
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.800, 19.400, 50.310
Angle α, β, γ (deg.)90.00, 109.90, 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*(BRU))-3'


Mass: 2887.600 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.: 61 / 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: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, Rhodium hexammine, lithium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Rhodium hexammine11
3lithium cacodylate11
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
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 5, 1995
Details: siliciu(111) curvated crystal plus multi-layer curvated mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→9.5 Å / Num. all: 6400 / Num. obs: 6312 / % possible obs: 98 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Redundancy: 9 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.043 / Net I/σ(I): 21
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 3.8 / Num. unique all: 997 / Rsym value: 0.138 / % possible all: 89
Reflection
*PLUS
% possible obs: 96 % / Redundancy: 6.2 % / Num. measured all: 40122

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
SHELXL-97refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 165D from pdb

165d


Resolution: 1.6→1.75 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4
Stereochemistry target values: personal dictionary from small molecules
Details: chain B (iso =11.8) is more agitated than chain A (iso =18.9)
RfactorNum. reflection% reflectionSelection details
Rfree0.196 529 -random
Rwork0.162 ---
all0.167 6346 --
obs0.161 6312 98 %-
Displacement parametersBiso mean: 16.3 Å2
Refinement stepCycle: LAST / Resolution: 1.6→1.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 389 19 61 469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_from_restr_planes0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDRfactor Rfree error% reflection obs (%)
1.6-1.750.1911250.147X-RAY DIFFRACTION0.0290
1.75-1.950.191010.153X-RAY DIFFRACTION0.0290
1.95-2.350.1931350.162X-RAY DIFFRACTION0.0297
2.35-3.050.197950.169X-RAY DIFFRACTION0.02100
3.05-9.50.22730.181X-RAY DIFFRACTION0.02100
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.05
X-RAY DIFFRACTIONs_chiral_restr0.093

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