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- PDB-4l26: Crystal structure of DNA duplex containing consecutive T-T mispai... -

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Basic information

Entry
Database: PDB / ID: 4l26
TitleCrystal structure of DNA duplex containing consecutive T-T mispairs (Br-derivative)
ComponentsDNA (5'-D(*CP*GP*(CBR)P*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 / MAD / Resolution: 1.4 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*(CBR)P*GP*AP*TP*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,4672
Polymers7,4672
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-1 kcal/mol
Surface area3710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.360, 39.310, 30.460
Angle α, β, γ (deg.)90.000, 99.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3733.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.16 Å3/Da / Density % sol: 43.17 %
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: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.0, 0.91942, 0.92006
DetectorDate: Oct 22, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.919421
30.920061
ReflectionResolution: 1.4→21.94 Å / Num. obs: 12212

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata reduction
CrystalCleardata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→21.94 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2662 1260 9.9 %
Rwork0.2323 --
obs-12212 96.4 %
Solvent computationBsol: 52.9486 Å2
Displacement parametersBiso max: 52.41 Å2 / Biso mean: 19.0444 Å2 / Biso min: 9.74 Å2
Baniso -1Baniso -2Baniso -3
1--1.441 Å20 Å29.21 Å2
2---3.437 Å20 Å2
3---4.878 Å2
Refinement stepCycle: LAST / Resolution: 1.4→21.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 135 621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.964
X-RAY DIFFRACTIONc_mcbond_it1.4941.5
X-RAY DIFFRACTIONc_mcangle_it1.9862
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 (%)
1.4-1.450.44951240.45961132125698
1.45-1.510.44321090.44391110121998
1.51-1.580.35531440.33371071121597.9
1.58-1.660.40391190.29341120123998.7
1.66-1.760.29831460.22341111125798.8
1.76-1.90.26251120.23091135124799
1.9-2.090.29551410.26931051119293.9
2.09-2.390.29651070.2241999110687.7
2.39-3.020.23791400.19911140128099.3
3.02-1000.18651180.17221083120192.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_free.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4brc.param

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