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- PDB-4l25: Crystal structure of DNA duplex containing consecutive T-T mispairs -

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Basic information

Entry
Database: PDB / ID: 4l25
TitleCrystal structure of DNA duplex containing consecutive T-T mispairs
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / T-T mispair / A-T-T triplet / non-helical DNA duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsKondo, J. / Yamada, T. / Hirose, C. / Tanaka, Y. / Ono, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-Hg(II) -T Base Pairs
Authors: Kondo, J. / Yamada, T. / Hirose, C. / Okamoto, I. / Tanaka, Y. / Ono, A.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*AP*TP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3092
Polymers7,3092
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area3970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.340, 39.330, 30.680
Angle α, β, γ (deg.)90.000, 98.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, ammonium chloride , 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-1A / Wavelength: 1 Å
DetectorDate: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→19.1 Å / Num. obs: 24441

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L26

4l26


Resolution: 1.1→19.08 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2405 2409 9.2 %
Rwork0.2305 --
obs-24438 93.1 %
Solvent computationBsol: 50.0215 Å2
Displacement parametersBiso max: 51.24 Å2 / Biso mean: 15.1144 Å2 / Biso min: 6.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.069 Å20 Å23.416 Å2
2---2.211 Å20 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 0 170 654
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.895
X-RAY DIFFRACTIONc_mcbond_it1.0131.5
X-RAY DIFFRACTIONc_mcangle_it1.4622
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.140.35212510.35272173242491.6
1.14-1.180.33172330.3192141237491.8
1.18-1.240.28162190.27562186240592.9
1.24-1.30.2842380.27752217245593.5
1.3-1.390.26252480.2692214246294.3
1.39-1.490.24822450.24322233247895.4
1.49-1.640.2442410.22622288252995.9
1.64-1.880.22322680.20392268253697.1
1.88-2.370.21842610.20442333259497.8
2.37-1000.22372050.21731976218181.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_free.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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