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- PDB-1d81: THE CONFORMATIONAL VARIABILITY OF AN ADENOSINE. INOSINE BASE-PAIR... -

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Basic information

Entry
Database: PDB / ID: 1d81
TitleTHE CONFORMATIONAL VARIABILITY OF AN ADENOSINE. INOSINE BASE-PAIR IN A SYNTHETIC DNA DODECAMER
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*IP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLeonard, G.A. / Booth, E.D. / Hunter, W.N. / Brown, T.
CitationJournal: Nucleic Acids Res. / Year: 1992
Title: The conformational variability of an adenosine.inosine base-pair in a synthetic DNA dodecamer.
Authors: Leonard, G.A. / Booth, E.D. / Hunter, W.N. / Brown, T.
History
DepositionJul 7, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1992Provider: 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 (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*IP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*IP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3452
Polymers7,3452
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)25.160, 41.060, 65.450
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 chain DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*IP*GP*CP*G)-3')


Mass: 3672.403 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4SPERMINE_HCL11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
10.5 mMprotein1drop
215 mMsodium cacodylate1drop
340 mMmagnesium chloride1drop
40.3 mMspermine-HCl1drop
650 %(v/v)1reservoir
5%(v/v)MPD1drop

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Data collection

DiffractionMean temperature: 277 K
DetectorType: SIEMENS AED2 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. all: 4866 / Num. obs: 2462 / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.09
Reflection
*PLUS
Num. all: 10292 / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.09

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.5→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.158 2004
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 488 0 71 559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.011
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.028
X-RAY DIFFRACTIONn_phos_bond_d0.011
X-RAY DIFFRACTIONn_phos_bond_angle_d0.025
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 7 Å / σ(F): 2 / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS

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