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- PDB-161d: A SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUC... -

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Basic information

Entry
Database: PDB / ID: 161d
TitleA SINGLE 2'-HYDROXYL GROUP CONVERTS B-DNA TO A-DNA: CRYSTAL STRUCTURE OF THE DNA-RNA CHIMERIC DECAMER DUPLEX D(CCGGC)R(G)D(CCGG) WITH A NOVEL INTERMOLECULAR G.C BASE-PAIRED QUADRUPLET
ComponentsDNA/RNA (5'-D(*CP*CP*GP*GP*CP*)-R(*GP*)-D(*CP*CP*GP*G)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBan, C. / Ramakrishnan, B. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: A single 2'-hydroxyl group converts B-DNA to A-DNA. Crystal structure of the DNA-RNA chimeric decamer duplex d(CCGGC)r(G)d(CCGG) with a novel intermolecular G-C base-paired quadruplet.
Authors: Ban, C. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionFeb 10, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0May 18, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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: DNA/RNA (5'-D(*CP*CP*GP*GP*CP*)-R(*GP*)-D(*CP*CP*GP*G)-3')
B: DNA/RNA (5'-D(*CP*CP*GP*GP*CP*)-R(*GP*)-D(*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1262
Polymers6,1262
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.630, 45.240, 47.990
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(*CP*CP*GP*GP*CP*)-R(*GP*)-D(*CP*CP*GP*G)-3')


Mass: 3062.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3SPERMINE_HCL11
4WATER12
5MPD12

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. all: 8769 / Num. obs: 2837 / Observed criterion σ(I): 1
Reflection
*PLUS
Rmerge(I) obs: 0.021

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 1.9→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.136 -
obs0.136 2753
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 406 0 61 467
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 2753 / σ(F): 1 / Rfactor obs: 136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_dihedral_angle_d31.4
X-RAY DIFFRACTIONx_dihedral_angle_deg3.4

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