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- PDB-1d90: REFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MI... -

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Basic information

Entry
Database: PDB / ID: 1d90
TitleREFINED CRYSTAL STRUCTURE OF AN OCTANUCLEOTIDE DUPLEX WITH I.T MISMATCHED BASE PAIRS
ComponentsDNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX / MODIFIED / MISMATCHED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsCruse, W.B.T. / Aymani, J. / Kennard, O. / Brown, T. / Jack, A.G.C. / Leonard, G.A.
CitationJournal: Nucleic Acids Res. / Year: 1989
Title: Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs.
Authors: Cruse, W.B. / Aymani, J. / Kennard, O. / Brown, T. / Jack, A.G. / Leonard, G.A.
History
DepositionOct 17, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: 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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3')
B: DNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.070, 45.070, 45.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain DNA (5'-D(*GP*GP*IP*GP*CP*TP*CP*C)-3')


Mass: 2428.590 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growMethod: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4WATER12
Crystal grow
*PLUS
pH: 6.5 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mloctamer1drop
250 mMsodium cacodylate1drop
3100 mM1drop0.002mlMgCl2
4water1drop

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: SIEMENS AED2 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.66 Å / Num. all: 5795 / Num. obs: 3310 / % possible obs: 57 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.04
Reflection
*PLUS
Observed criterion σ(F): 1 / Rmerge(I) obs: 0.04

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.14 2853
Refine Biso Class: ALL ATOMS / Details: TR / Treatment: isotropic
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 81 403
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 10 Å / σ(F): 2 / Num. reflection obs: 2853 / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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