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- PDB-223d: DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMIN... -

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Basic information

Entry
Database: PDB / ID: 223d
TitleDIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMINE ANALOGUE WITH GUANINE IN A DNA Z-FORM DUPLEX: SIGNIFICANCE FOR BASE ANALOGUE MUTAGENESIS
ComponentsDNA (5'-D(*CP*GP*CP*GP*(C46)P*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoore, M.H. / Van Meervelt, L. / Salisbury, S.A. / Kong Thoo Lin, P. / Brown, D.M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form duplex: significance for base analogue mutagenesis.
Authors: Moore, M.H. / Van Meervelt, L. / Salisbury, S.A. / Lin, P.K. / Brown, D.M.
#1: Journal: Nucleosides and Nucleotides / Year: 1995
Title: To Wobble or Not to Wobble: Modified Bases Incorporated Into DNA
Authors: Van Meervelt, L. / Moore, M.H. / Kong Thoo Lin, P. / Brown, D.M.
History
DepositionAug 1, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 9, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 14, 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*CP*GP*(C46)P*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*(C46)P*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,7042
Polymers3,7042
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.230, 30.630, 43.780
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*GP*(C46)P*G)-3')


Mass: 1852.242 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.65 Å3/Da / Density % sol: 25.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4WATER12
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMoligonucleotide1drop
225 mMsodium cacodylate1drop
315 mM1dropMgCl2
450 %(v/v)MPD1reservoir
51

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Rmerge(I) obs: 0.004

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Processing

Software
NameClassification
MERLOTphasing
NUCLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ZDF002

Resolution: 1.7→8 Å / σ(F): 4 /
RfactorNum. reflection% reflection
obs0.179 2798 100 %
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 6 51 297
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_it4.797.5
X-RAY DIFFRACTIONn_sugar_angle_it5.747.5
X-RAY DIFFRACTIONn_phos_bond_it10.387.5
X-RAY DIFFRACTIONn_phos_angle_it7.717.5
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0410.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0760.05
X-RAY DIFFRACTIONn_phos_bond_d0.0710.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0480.025
X-RAY DIFFRACTIONn_plane_restr0.0440.03
X-RAY DIFFRACTIONn_chiral_restr0.1380.1
X-RAY DIFFRACTIONn_singtor_nbd0.1450.063
X-RAY DIFFRACTIONn_multtor_nbd0.2780.063
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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