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- PDB-6l75: Crystal structure of d(GTGGGCCGAC)2 DNA duplex -

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Basic information

Entry
Database: PDB / ID: 6l75
TitleCrystal structure of d(GTGGGCCGAC)2 DNA duplex
Components(DNA (5'-D(P*GP*TP*GP*GP*GP*CP*CP*GP*AP*C)-3')) x 2
KeywordsDNA / A form DNA / GGGGCC motif / GC rich duplex / G4C2
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.578 Å
AuthorsHou, M.H. / Satange, R.B. / Zeng, J.Y.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction.
Authors: Jhan, C.R. / Satange, R. / Wang, S.C. / Zeng, J.Y. / Horng, Y.C. / Jin, P. / Neidle, S. / Hou, M.H.
History
DepositionOct 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7 kcal/mol
Surface area3790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.457, 38.457, 79.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 3086.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*GP*TP*GP*GP*GP*CP*CP*GP*AP*C)-3')


Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1mM DNA, 100mM Licl, 10mM MnCl2, 50mM MES (pH 6.5), 2.6M Sodium malonate dibasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 9886 / % possible obs: 99.4 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Rrim(I) all: 0.055 / Χ2: 0.979 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.6410.20.3769640.9720.1230.3960.63899.8
1.64-1.710.70.219710.9920.0670.220.776100
1.7-1.7810.70.1759700.9930.0570.1850.987100
1.78-1.8710.70.1429710.9960.0460.1491.062100
1.87-1.9910.60.1219770.9960.0390.1271.04100
1.99-2.1410.10.0969840.9970.0320.1011.043100
2.14-2.369.90.0719950.9980.0240.0751.027100
2.36-2.79.30.0599930.9980.020.0621.11499.7
2.7-3.48.30.04810080.9980.0180.0511.05699
3.4-3080.03810530.9990.0140.0411.09196.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A DNA

Resolution: 1.578→20.806 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.96
RfactorNum. reflection% reflection
Rfree0.2276 981 9.95 %
Rwork0.1991 --
obs0.2019 9855 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.26 Å2 / Biso mean: 30.0366 Å2 / Biso min: 18.54 Å2
Refinement stepCycle: final / Resolution: 1.578→20.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 0 124 534
Biso mean---40.44 -
Num. residues----20
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5781-1.6610.21351400.1965121898
1.661-1.7650.24381380.20611252100
1.765-1.90120.30841370.2311261100
1.9012-2.09230.26791340.2361251100
2.0923-2.39470.26811410.22061283100
2.3947-3.01560.27861400.25371283100
3.0156-20.80.18231510.161132697

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