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

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Basic information

Entry
Database: PDB / ID: 3gjk
Titlecrystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
Components
  • 5'-D(*CP*GP*CP*GP*AP*A)-3'
  • 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3'
KeywordsDNA / duplex / bicyclic cytosine / 7 / 8-dihydropyridol[2 / 3-d]pyrimidin-2-one
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTakenaka, A. / Juan, E.C.M. / Shimizu, S. / Haraguchi, T. / Xiao, M. / Kurose, T. / Ohkubo, A. / Sekine, M. / Shibata, T. / Millington, C.L. / Williams, D.M.
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.M.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,6963
Polymers3,6562
Non-polymers391
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-2 kcal/mol
Surface area2660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.221, 26.221, 99.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-13-

K

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Components

#1: DNA chain 5'-D(*CP*GP*CP*GP*AP*A)-3'


Mass: 1818.231 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3'


Mass: 1838.251 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mM Sodium cacodylate (pH7.0), 6mM Spermine tetrahydrochloride, 6mM NaCl, 40mM KCl, 5% MPD , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 31, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 2137 / Num. obs: 2137 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 70.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 11.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ehv

1ehv


Resolution: 2.2→18.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.241 / SU ML: 0.215 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.272 / ESU R Free: 0.249 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.314 92 4.5 %RANDOM
Rwork0.252 ---
all0.261 2110 --
obs0.255 2071 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.346 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.84 Å20 Å2
2--1.68 Å20 Å2
3----2.52 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 246 1 35 282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.023328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg4.3513415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1440.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.02126
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.30.271
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3630.2164
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.26
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3950.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5150.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4310.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.9050.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it3.5843304
X-RAY DIFFRACTIONr_scangle_it4.8794.5415
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.543 4 -
Rwork0.475 148 -
obs--100 %

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