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- PDB-165d: THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RE... -

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Basic information

Entry
Database: PDB / ID: 165d
TitleTHE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE
ComponentsDNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX / OVERHANGING BASES / MODIFIED / MISMATCHED
Function / homologyRHODIUM HEXAMINE ION / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsCruse, W. / Saludjian, P. / Biala, E. / Strazewski, P. / Prange, T. / Kennard, O.
CitationJournal: 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 21, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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: DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')
B: DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5966
Polymers5,7752
Non-polymers8204
Water97354
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, 50.140
Angle α, β, γ (deg.)90.00, 109.90, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED ...1: THE DEOXY-BROMO-URACIL +U IS WELL ORDERED ON STRAND A BUT NOT ON STRAND B (RESIDUE +U 18) WHERE TWO (50:50) DISORDERED POSITIONS WERE GIVEN. FOUR RHODIUM HEXAMINE IONS RH(NH3)6 ++ WERE LOCATED (NAMED RHD), TWO WITH FULL OCCUPANCY FACTORS (RESIDUES 19 AND 20) AND TWO WITH PARTIAL OCCUPANCIES (RESIDUES 21 AND 22).
Components on special symmetry positions
IDModelComponents
11B-18-

BRU

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Components

#1: RNA chain DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3')


Mass: 2887.600 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-RHD / RHODIUM HEXAMINE ION


Mass: 205.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H18N6Rh
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2LI CACODYLATE11
3[RH(NH3)6]CL311
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 %MPD1reservoir
20.1 mgnonamer1drop
320 mMlithium cacodylate1drop
46-10 mM1dropcan be replaced by Ir(NH3)6Cl3Rh(NH3)6Cl3

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteTypeID
SYNCHROTRONLURE LURE 1
2
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
ENRAF-NONIUS FAST2DIFFRACTOMETER
Radiation
IDMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Mx-ray1
2Mx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionHighest resolution: 1.6 Å / Num. obs: 6093 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.6 Å

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.55→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.18 -
obs0.18 6098
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 389 31 54 474
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d0.03
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d0.0110.015
X-RAY DIFFRACTIONn_angle_d0.0280.025
X-RAY DIFFRACTIONn_angle_deg
X-RAY DIFFRACTIONn_dihedral_angle_d
X-RAY DIFFRACTIONn_improper_angle_d
X-RAY DIFFRACTIONn_planar_d0.0360.04
X-RAY DIFFRACTIONn_plane_restr0.0120.02
X-RAY DIFFRACTIONn_chiral_restr0.0740.07
X-RAY DIFFRACTIONn_mcbond_it1.5082
X-RAY DIFFRACTIONn_scbond_it2.1242
X-RAY DIFFRACTIONn_mcangle_it2.3173
X-RAY DIFFRACTIONn_scangle_it3.3733

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