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- PDB-332d: CRYSTAL STRUCTURE OF R(GUGUGUA)D(C) WITH TANDEM G-U/U-G WOBBLE PA... -

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Basic information

Entry
Database: PDB / ID: 332d
TitleCRYSTAL STRUCTURE OF R(GUGUGUA)D(C) WITH TANDEM G-U/U-G WOBBLE PAIRS WITH STRAND SLIPPAGE
ComponentsDNA/RNA (5'-R(*GP*UP*GP*UP*GP*UP*AP*)-D(*C)-3')
KeywordsDNA/RNA / A-DNA/RNA / DOUBLE HELIX / OVERHANGING BASE / DNA-RNA complex
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsBiswas, R. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of r(GUGUGUA)dC with tandem G x U/U x G wobble pairs with strand slippage.
Authors: Biswas, R. / Sundaralingam, M.
History
DepositionMay 14, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 23, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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*UP*GP*UP*GP*UP*AP*)-D(*C)-3')
B: DNA/RNA (5'-R(*GP*UP*GP*UP*GP*UP*AP*)-D(*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0552
Polymers5,0552
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.820, 40.820, 66.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-22-

HOH

21B-31-

HOH

31B-45-

HOH

41B-75-

HOH

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*GP*UP*GP*UP*GP*UP*AP*)-D(*C)-3')


Mass: 2527.545 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4[CO(NH3)6]3+11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 mMRNA1dropsingle strand concentration
20.5 mMcobaltic hexammine chloride1drop
340 mMsodium cacodylate1drop
410 %(v/v)MPD1drop
555 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRsym value: 0.0468
Reflection
*PLUS
Highest resolution: 1.58 Å / Num. obs: 4314 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.0468

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Processing

Software
NameVersionClassification
X-PLOR3refinement
XENGENV. 2.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AHH077

Resolution: 1.58→8 Å / σ(F): 1.5
RfactorNum. reflection
Rfree0.277 -
Rwork0.212 -
obs0.212 4314
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.58→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 334 0 71 405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
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
LS refinement shellResolution: 1.38→1.58 Å
Xplor fileSerial no: 1 / Param file: PARAM_ND.DNA / Topol file: TOPOLOGY.DNA
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.58 Å / Lowest resolution: 8 Å / σ(F): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS

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