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- PDB-246d: STRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, ... -

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Basic information

Entry
Database: PDB / ID: 246d
TitleSTRUCTURE OF THE PURINE-PYRIMIDINE ALTERNATING RNA DOUBLE HELIX, R(GUAUAUA)D(C) , WITH A 3'-TERMINAL DEOXY RESIDUE
ComponentsDNA/RNA (5'-R(*GP*UP*AP*UP*AP*UP*AP*)-D(*C)-3')
KeywordsDNA/RNA / A-DNA/RNA / DOUBLE HELIX / DNA-RNA complex
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWahl, M.C. / Ban, C. / Sekharudu, C. / Ramakrishnan, B. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue.
Authors: Wahl, M.C. / Ban, C. / Sekharudu, C. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionJan 25, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 26, 1996Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*UP*AP*)-D(*C)-3')
B: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*UP*AP*)-D(*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0374
Polymers4,9912
Non-polymers462
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.100, 43.100, 59.400
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-17-

NA

21B-18-

NA

31A-103-

HOH

41B-102-

HOH

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Components

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


Mass: 2495.545 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 42.18 %
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: 295 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMoligonucleotide1drop
26 mMcobaltic hexamine trichloride1drop0.5 ml
3100 mMsodium cacodylate1drop0.001 ml
4water1drop0.005 ml
5MPD1drop0.001 ml
660 %1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 17, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 1775 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0171
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. all: 2076 / % possible obs: 85.5 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
X-PLOR3refinement
XENGENV. 2.0data reduction
RefinementResolution: 2.2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.156 --
obs0.156 1775 86 %
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 330 2 85 417
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_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.55
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 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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