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- PDB-1d97: CHIRAL PHOSPHOROTHIOATE ANALOGUES OF B-DNA: THE CRYSTAL STRUCTURE... -

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Basic information

Entry
Database: PDB / ID: 1d97
TitleCHIRAL PHOSPHOROTHIOATE ANALOGUES OF B-DNA: THE CRYSTAL STRUCTURE OF RP-D(GP(S) CPGP(S)CPGP(S)C)
ComponentsDNA (5'-D(RP*GP*(SC)P*GP*(SC)P*GP*(SC))-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.17 Å
AuthorsCruse, W.B.T. / Salisbury, S.A. / Brown, T. / Cosstick, R. / Eckstein, F. / Kennard, O.
CitationJournal: J.Mol.Biol. / Year: 1986
Title: Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-d[Gp(S)CpGp(S)CpGp(S)C].
Authors: Cruse, W.B. / Salisbury, S.A. / Brown, T. / Cosstick, R. / Eckstein, F. / Kennard, O.
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(RP*GP*(SC)P*GP*(SC)P*GP*(SC))-3')
B: DNA (5'-D(RP*GP*(SC)P*GP*(SC)P*GP*(SC))-3')


Theoretical massNumber of molelcules
Total (without water)3,7172
Polymers3,7172
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.900, 39.150, 20.640
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(RP*GP*(SC)P*GP*(SC)P*GP*(SC))-3')


Mass: 1858.403 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 1.9 Å3/Da / Density % sol: 35.16 %
Crystal growTemperature: 287 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 287.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2ISOPROPANOL11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMoligonucleotide1dropcan be replaced with ammonium salt
2100 mMsodium cacodylate1drop
30.75 mM1dropMgCl2
41.25 mMspermine hydrochloride1drop
510 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 291 K
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.17→25 Å / Num. obs: 1954
Reflection
*PLUS
Highest resolution: 2.17 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.24

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.17→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.145 1327
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.17→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 234 6 72 312
Refinement
*PLUS
Highest resolution: 2.17 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection obs: 1327 / Rfactor obs: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS

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