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- PDB-205d: STRUCTURE OF AN RNA DOUBLE HELIX INCLUDING URACIL-URACIL BASE PAI... -

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Basic information

Entry
Database: PDB / ID: 205d
TitleSTRUCTURE OF AN RNA DOUBLE HELIX INCLUDING URACIL-URACIL BASE PAIRS IN AN INTERNAL LOOP
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*UP*UP*GP*GP*UP*CP*C)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX / INTERNAL LOOP / MISMATCHED
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.64 Å
AuthorsBaeyens, K.J. / De Bondt, H.L. / Holbrook, S.R.
CitationJournal: Nat.Struct.Biol. / Year: 1995
Title: Structure of an RNA double helix including uracil-uracil base pairs in an internal loop.
Authors: Baeyens, K.J. / De Bondt, H.L. / Holbrook, S.R.
History
DepositionApr 14, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*CP*UP*UP*UP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*UP*UP*GP*GP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,6112
Polymers7,6112
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.440, 32.440, 85.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*CP*UP*UP*UP*GP*GP*UP*CP*C)-3')


Mass: 3805.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.95 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6 / Details: pH 5.60, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG11
3EDTA11
4NH4 ACETATE11
5NA CITRATE11
6SPERMINE_HCL11
7WATER12
8PEG12
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMRNA1drop
20.1 mMEDTA1drop
30.2 Mammonium acetate1reservoir
40.1 Msodium citrate1reservoirpH5.6
530 %PEG40001reservoir
68 mMspermine tetrahydrochloride1reservoir
71
81

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Type: SSRL
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.64 Å / Num. obs: 2415 / % possible obs: 90.1 % / Observed criterion σ(I): 2.6 / Rmerge(I) obs: 0.108
Reflection
*PLUS
Highest resolution: 2.64 Å / % possible obs: 90.1 % / Observed criterion σ(I): 2.6

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.64→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 2233
Refinement stepCycle: LAST / Resolution: 2.64→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 502 0 39 541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.028
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
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
Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.64 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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