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- PDB-3ajl: Crystal structure of d(CGCGGATf5UCGCG): 5-Formyluridine:guanosine... -

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Basic information

Entry
Database: PDB / ID: 3ajl
TitleCrystal structure of d(CGCGGATf5UCGCG): 5-Formyluridine:guanosine Base-pair in B-DNA with DAPI
Components5'-D(*CP*GP*CP*GP*GP*AP*TP*(UFR)P*CP*GP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX
Function / homology6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTsunoda, M. / Sakaue, T. / Ueno, Y. / Matsuda, A. / Takenaka, A.
CitationJournal: J Nucleic Acids / Year: 2010
Title: Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil
Authors: Tsunoda, M. / Sakaue, T. / Naito, S. / Sunami, T. / Abe, N. / Ueno, Y. / Matsuda, A. / Takenaka, A.
History
DepositionJun 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: 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 / 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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,6884
Polymers7,3872
Non-polymers3022
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint3 kcal/mol
Surface area4330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.003, 40.501, 66.773
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*GP*AP*TP*(UFR)P*CP*GP*CP*G)-3'


Mass: 3693.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA
#2: Chemical ChemComp-DAP / 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DAPI


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20mM Na cacodylate, 6mM spermine, 40mM NaCl, 10mM MgCl2, 5% MPD, 0.5mM DAPI, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→34.7 Å / Num. obs: 2342 / % possible obs: 99.9 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.063 / Net I/σ(I): 6.7
Reflection shellResolution: 2.6→2.74 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.2 / Num. unique all: 333 / Rsym value: 0.349 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNS1.2refinement
DPSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 355D

355d


Resolution: 2.7→9.86 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 229102.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.281 189 9.4 %RANDOM
Rwork0.212 ---
obs0.212 2021 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.1181 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.68 Å20 Å20 Å2
2---1.03 Å20 Å2
3----11.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→9.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 490 22 45 557
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.077 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.469 37 11.6 %
Rwork0.39 283 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3formylu.paramformylu.top
X-RAY DIFFRACTION4dapi.paramdapi.top
X-RAY DIFFRACTION5noNH.paramnoNH.top

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