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- PDB-7t6y: d((CGA)5TGA) parallel-stranded homo-duplex -

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Basic information

Entry
Database: PDB / ID: 7t6y
Titled((CGA)5TGA) parallel-stranded homo-duplex
ComponentsDNA (5'-D(*CP*GP*AP*CP*GP*AP*CP*GP*AP*CP*GP*AP*CP*GP*AP*TP*GP*A)-3')
KeywordsDNA / triplet repeat DNA / parallel-stranded duplex / non-canonical DNA / d(CGA)
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLuteran, E.M. / Paukstelis, P.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The parallel-stranded d(CGA) duplex is a highly predictable structural motif with two conformationally distinct strands.
Authors: Luteran, E.M. / Paukstelis, P.J.
History
DepositionDec 14, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionDec 22, 2021ID: 7SB9
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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(*CP*GP*AP*CP*GP*AP*CP*GP*AP*CP*GP*AP*CP*GP*AP*TP*GP*A)-3')
B: DNA (5'-D(*CP*GP*AP*CP*GP*AP*CP*GP*AP*CP*GP*AP*CP*GP*AP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0819
Polymers11,1192
Non-polymers9617
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.499, 32.350, 32.260
Angle α, β, γ (deg.)90.000, 91.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-259-

HOH

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Components

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


Mass: 5559.620 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% MPD, 120 mM barium chloride, 30 mM sodium cacodylate, equilibrated against 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→32.255 Å / Num. obs: 3487 / % possible obs: 87.2 % / Redundancy: 1.8 % / CC1/2: 0.94 / Rpim(I) all: 0.109 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 350 / CC1/2: 0.395 / Rpim(I) all: 0.288

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IXJ

1ixj


Resolution: 2.3→32.255 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2417 161 4.62 %
Rwork0.204 3326 -
obs0.2058 3487 87.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.02 Å2 / Biso mean: 13.2239 Å2 / Biso min: 1.79 Å2
Refinement stepCycle: final / Resolution: 2.3→32.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 740 10 119 869
Biso mean--15.3 17.97 -
Num. residues----36
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009834
X-RAY DIFFRACTIONf_angle_d0.9981284
X-RAY DIFFRACTIONf_dihedral_angle_d31.51352
X-RAY DIFFRACTIONf_chiral_restr0.059142
X-RAY DIFFRACTIONf_plane_restr0.00836
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 87 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3001-2.89760.2713830.22511642
2.8976-32.2550.2246780.19141684

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