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- PDB-3f8o: Structure of d(CACGCG).d(CGCGTG) with low concentration of PdCl2 -

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Basic information

Entry
Database: PDB / ID: 3f8o
TitleStructure of d(CACGCG).d(CGCGTG) with low concentration of PdCl2
Components
  • DNA (5'-D(*DCP*DAP*DCP*DGP*DCP*DG)-3')
  • DNA (5'-D(*DCP*DGP*DCP*DGP*DTP*DG)-3')
KeywordsDNA / Z-DNA double helix
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMandal, P.K. / Venkadesh, S. / Gautham, N.
CitationJournal: To be Published
Title: Crystal structures of d(CACGCG).d(CGCGTG) grown with different metal ions
Authors: Mandal, P.K. / Venkadesh, S. / Gautham, N.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 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(*DCP*DAP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DTP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)3,6192
Polymers3,6192
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-5 kcal/mol
Surface area2340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)17.785, 30.941, 44.789
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(*DCP*DAP*DCP*DGP*DCP*DG)-3')


Mass: 1794.206 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DCP*DGP*DCP*DGP*DTP*DG)-3')


Mass: 1825.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.702381 Å3/Da / Density % sol: 27.748251 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 50mM Sodium Cacodylate, 0.1mM PdCl2, 1.0mM spermine, 40% (v/v) MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3PdCl211
4spermine11
5H2O11
6MPD12
7sodium cacodylate12
8PdCl212
9H2O12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→25.5 Å / Num. all: 2822 / Num. obs: 2809 / % possible obs: 97.9 % / Redundancy: 4.27 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.0482 / Net I/σ(I): 5.7
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.8 / Num. unique all: 279 / Rsym value: 0.2904 / % possible all: 96.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fiber model of Z-DNA built using insightII

Resolution: 1.72→25.46 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.91 / SU ML: 0.087 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23992 127 4.5 %RANDOM
Rwork0.21804 ---
obs0.21906 2682 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.72→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 246 0 27 273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021276
X-RAY DIFFRACTIONr_angle_refined_deg2.0393426
X-RAY DIFFRACTIONr_chiral_restr0.0770.248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02125
X-RAY DIFFRACTIONr_nbd_refined0.1750.280
X-RAY DIFFRACTIONr_nbtor_refined0.2770.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.29
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0480.23
X-RAY DIFFRACTIONr_scbond_it1.8943402
X-RAY DIFFRACTIONr_scangle_it2.2624.5424
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 7 -
Rwork0.334 182 -
obs-182 94.97 %

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