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- PDB-433d: CRYSTAL STRUCTURE OF A 14 BASE PAIR RNA DUPLEX WITH NONSYMMETRICA... -

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Basic information

Entry
Database: PDB / ID: 433d
TitleCRYSTAL STRUCTURE OF A 14 BASE PAIR RNA DUPLEX WITH NONSYMMETRICAL TANDEM G.U WOBBLE BASE PAIRS
Components5'-R(*GP*GP*UP*AP*UP*UP*GP*CP*GP*GP*UP*AP*CP*C)-3'
KeywordsRNA / TANDEM NONSYMMETRICAL G.U WOBBLE BASE PAIR
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTrikha, J. / Filman, D.J. / Hogle, J.M.
CitationJournal: Nucleic Acids Res. / Year: 1999
Title: Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem GxU wobble base pairs.
Authors: Trikha, J. / Filman, D.J. / Hogle, J.M.
History
DepositionOct 22, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 4, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: 5'-R(*GP*GP*UP*AP*UP*UP*GP*CP*GP*GP*UP*AP*CP*C)-3'
B: 5'-R(*GP*GP*UP*AP*UP*UP*GP*CP*GP*GP*UP*AP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)8,9592
Polymers8,9592
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.4, 45.4, 147.9
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number182
Cell settinghexagonal
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-51-

HOH

21A-52-

HOH

31A-53-

HOH

41B-61-

HOH

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Components

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


Mass: 4479.691 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MPD11
3MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlRNA1drop
250 mMsodium cacodylate1drop
315 %1drop
4100 mMsodium cacodylate1reservoir
530 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Sep 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 4969 / Num. obs: 4969 / % possible obs: 84.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.028
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.051 / % possible all: 44
Reflection
*PLUS
% possible obs: 85.6 % / Num. measured all: 18099
Reflection shell
*PLUS
% possible obs: 44 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.277 498 10 %
Rwork0.225 --
obs0.225 4859 84.3 %
all-4859 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 592 0 72 664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.22
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: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.54
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg7.55

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