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- PDB-4itd: Structures of DNA duplexes containing O6-carboxymethylguanine, a ... -

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Basic information

Entry
Database: PDB / ID: 4itd
TitleStructures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing transition mutation
ComponentsDNA (5'-D(*CP*GP*CP*GP*(C6G)P*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / damaged DNA / O6-carboxymethylguanine / mutagenesis
Function / homologyChem-HT / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsZhang, F. / Suzuki, K. / Tsunoda, M. / Wilkinson, O. / Millington, C.L. / Williams, D.M. / Morishita, E.C. / Takenaka, A.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations
Authors: Zhang, F. / Tsunoda, M. / Suzuki, K. / Kikuchi, Y. / Wilkinson, O. / Millington, C.L. / Margison, G.P. / Williams, D.M. / Czarina Morishita, E. / Takenaka, A.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _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: DNA (5'-D(*CP*GP*CP*GP*(C6G)P*AP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*(C6G)P*AP*TP*TP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9244
Polymers7,4752
Non-polymers4492
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-11 kcal/mol
Surface area5200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.051, 40.404, 65.667
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*(C6G)P*AP*TP*TP*CP*GP*CP*G)-3')


Mass: 3737.427 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-HT / 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / HOECHST 33258


Mass: 424.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10%(v/v)MPD, 12mM spermine 4HCL, 80mM NaCL, 12mM KCL, 20mM MgCL2, 40mM Na cacodylate(pH7.0), 1mM Hoechst 33258, 1mM DNA, vapor diffusion, hanging drop, temperature 277K

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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 315r / Detector: CCD / Date: Mar 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 4877 / % possible obs: 91 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Diffraction-ID% possible allRmerge(I) obs
1.94-1.971.4133.7
1.97-2.011.8152.6
2.01-2.052.4169.3
2.05-2.093177.8
2.09-2.143.7191.6
2.14-2.184.6196
2.18-2.245.5198.8
2.24-2.36.11100
2.3-2.376.6199.6
2.37-2.446.611000.951
2.44-2.536.711000.641
2.53-2.636.811000.417
2.63-2.756.711000.26
2.75-2.96.911000.205
2.9-3.086.811000.146
3.08-3.326.6199.20.053
3.32-3.656.6199.70.047
3.65-4.186.411000.042
4.18-5.266.311000.039
5.26-505.61950.036

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→34.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.113 / SU ML: 0.2 / SU R Cruickshank DPI: 0.3415 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25351 188 4.9 %RANDOM
Rwork0.22611 ---
obs0.22763 3654 72.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.682 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å2-0 Å2
2---0.98 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.94→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 496 33 80 609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.011583
X-RAY DIFFRACTIONr_bond_other_d0.0350.02292
X-RAY DIFFRACTIONr_angle_refined_deg2.1681.27894
X-RAY DIFFRACTIONr_angle_other_deg4.8733685
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_restr0.1090.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02318
X-RAY DIFFRACTIONr_gen_planes_other0.0310.02134
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
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_it4.1813589
X-RAY DIFFRACTIONr_scangle_it5.744.5894
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.557 2 -
Rwork0.514 79 -
obs--21.37 %

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