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- PDB-3gjh: Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2... -

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Basic information

Entry
Database: PDB / ID: 3gjh
TitleCrystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
Components5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'
KeywordsDNA / DNA duplex / bicyclic cytosine / 7 / 8-dihydropyridol[2 / 3-d]pyrimidin-2-one
Function / homology6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTakenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T.
CitationJournal: To be Published
Title: Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
Authors: Takenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T. / Ohkubo, A. / Sekine, M. / Shibata, T. / Millington, C.L.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6803
Polymers7,4032
Non-polymers2771
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint7 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.207, 41.379, 64.866
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 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'


Mass: 3701.440 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-DAP / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20mM Sodium cacodylate (pH7.0), 6mM Spermine tetrahydrochloride, 40mM KCl, 0.2% CHAPSO, 0.30mM DAPI, 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 1708 / Num. obs: 1708 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 38.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D30

1d30


Resolution: 2.9→10 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.306 157 -Random
Rwork0.259 ---
all-1689 --
obs-1629 99.3 %-
Displacement parametersBiso mean: 43.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 21 16 529
LS refinement shellResolution: 2.9→3.08 Å
RfactorNum. reflection% reflection
Rfree0.597 31 -
Rwork0.578 --
obs-228 95.9 %

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