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- PDB-168d: STABILIZING EFFECTS OF THE RNA 2'-SUBSTITUENT: CRYSTAL STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 168d
TitleSTABILIZING EFFECTS OF THE RNA 2'-SUBSTITUENT: CRYSTAL STRUCTURE OF AN OLIGODEOXYNUCLEOTIDE DUPLEX CONTAINING 2'-O-METHYLATED ADENOSINES
ComponentsDNA/RNA (5'-D(*GP*CP*GP*TP*)-R(*(A2M)P*)-D(*TP*AP*CP*GP*C)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX / MODIFIED / DNA-RNA HYBRID COMPLEX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLubini, P. / Zuercher, W. / Egli, M.
CitationJournal: Chem.Biol. / Year: 1994
Title: Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines.
Authors: Lubini, P. / Zurcher, W. / Egli, M.
History
DepositionApr 8, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA (5'-D(*GP*CP*GP*TP*)-R(*(A2M)P*)-D(*TP*AP*CP*GP*C)-3')
B: DNA/RNA (5'-D(*GP*CP*GP*TP*)-R(*(A2M)P*)-D(*TP*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,1502
Polymers6,1502
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.130, 45.649, 47.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-D(*GP*CP*GP*TP*)-R(*(A2M)P*)-D(*TP*AP*CP*GP*C)-3')


Mass: 3075.031 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2 Å / Num. all: 9702 / Num. obs: 3576

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Processing

Software
NameVersionClassification
PROLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementResolution: 2→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.193 3188
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 0 53 461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.1
X-RAY DIFFRACTIONp_chiral_restr0.14
X-RAY DIFFRACTIONp_singtor_nbd0.16
X-RAY DIFFRACTIONp_multtor_nbd0.12
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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