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- PDB-315d: CRYSTAL STRUCTURE OF AN ALTERNATING OCTAMER R(GUAUGUA)D(C) WITH A... -

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Basic information

Entry
Database: PDB / ID: 315d
TitleCRYSTAL STRUCTURE OF AN ALTERNATING OCTAMER R(GUAUGUA)D(C) WITH ADJACENT G-U WOBBLE PAIRS
ComponentsDNA/RNA (5'-R(*GP*UP*AP*UP*GP*UP*AP*)-D(*C)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsBiswas, R. / Wahl, M.C. / Ban, C. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of an alternating octamer r(GUAUGUA)dC with adjacent G x U wobble pairs
Authors: Biswas, R. / Wahl, M.C. / Ban, C. / Sundaralingam, M.
History
DepositionFeb 26, 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*AP*UP*GP*UP*AP*)-D(*C)-3')
B: DNA/RNA (5'-R(*GP*UP*AP*UP*GP*UP*AP*)-D(*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,0232
Polymers5,0232
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.710, 39.710, 68.150
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
11A-79-

HOH

21A-81-

HOH

31A-82-

HOH

41B-80-

HOH

51B-83-

HOH

61B-84-

HOH

71B-85-

HOH

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Components

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


Mass: 2511.545 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.25 %
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-ID
11 mMRNA1drop
20.5 mMcobaltic hexammine chloride1drop
340 mMsodium cacodylate1drop
410 %(v/v)MPD1drop
560 %(v/v)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
ReflectionHighest resolution: 1.38 Å / Num. obs: 5744 / Observed criterion σ(F): 1.5 / Rsym value: 0.0347
Reflection
*PLUS
Observed criterion σ(F): 1.5 / Rmerge(I) obs: 0.0349

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Processing

Software
NameVersionClassification
X-PLOR3refinement
XENGENV. 2.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AHH071

Resolution: 1.38→10 Å / σ(F): 1.5
RfactorNum. reflection
Rfree0.231 -
Rwork0.176 -
obs0.176 4035
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.38→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 332 0 69 401
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.3
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 1.5
Solvent computation
*PLUS
Displacement parameters
*PLUS

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