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- PDB-285d: X-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR ... -

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Basic information

Entry
Database: PDB / ID: 285d
TitleX-RAY AND SOLUTION STUDIES OF DNA OLIGOMERS AND IMPLICATIONS FOR THE STRUCTURAL BASIS OF A-TRACT-DEPENDENT CURVATURE
ComponentsDNA (5'-D(*CP*GP*CP*AP*IP*AP*TP*(5CM)P*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShatzky-Schwartz, M. / Shakked, Z. / Luisi, B.F.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature.
Authors: Shatzky-Schwartz, M. / Arbuckle, N.D. / Eisenstein, M. / Rabinovich, D. / Bareket-Samish, A. / Haran, T.E. / Luisi, B.F. / Shakked, Z.
History
DepositionSep 11, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0May 8, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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*IP*AP*TP*(5CM)P*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*IP*AP*TP*(5CM)P*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.400, 40.215, 65.268
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*IP*AP*TP*(5CM)P*TP*GP*CP*G)-3')


Mass: 3662.405 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE_HCL11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlDNA1drop
212.5 mM1dropMgCl2
31.2 mMspermine-4HCl1drop
420 mMsodium cacodylate1drop
510 %(w/v)MPD1drop
630 %(w/v)MPD1reservoir
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Jun 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 2152 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 4.05 % / Rmerge(I) obs: 0.0843
Reflection
*PLUS
Highest resolution: 2.5 Å
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 60 %

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Processing

Software
NameClassification
NUCLSQrefinement
XENGENdata reduction
ULTIMAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B-DNA ORIENTED FIBER

Resolution: 2.5→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.206 2043
Displacement parametersBiso mean: 14.6 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 2 98 584
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_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_d0.0110.03
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0370.06
X-RAY DIFFRACTIONn_phos_bond_d0.0330.05
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0780.1
X-RAY DIFFRACTIONn_plane_restr0.0190.04
X-RAY DIFFRACTIONn_chiral_restr0.2550.4
X-RAY DIFFRACTIONn_singtor_nbd0.0710.1
X-RAY DIFFRACTIONn_multtor_nbd0.0680.1
X-RAY DIFFRACTIONn_xhyhbond_nbd0.0710.1
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection all: 2152 / σ(F): 2 / Rfactor all: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.6 Å2
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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