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- PDB-6tzs: A DNA i-motif/duplex hybrid -

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Basic information

Entry
Database: PDB / ID: 6tzs
TitleA DNA i-motif/duplex hybrid
ComponentsDNA (5'-D(*CP*CP*AP*GP*GP*CP*TP*GP*(CBR)P*AP*A)-3')
KeywordsDNA / i-motif / duplex / quadruplex / hybrid / noncanonical
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsChu, B. / Paukstelis, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1149665 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A DNA G-quadruplex/i-motif hybrid.
Authors: Chu, B. / Zhang, D. / Paukstelis, P.J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
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.year / _citation_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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*CP*AP*GP*GP*CP*TP*GP*(CBR)P*AP*A)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*CP*TP*GP*(CBR)P*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)6,8442
Polymers6,8442
Non-polymers00
Water1267
1
A: DNA (5'-D(*CP*CP*AP*GP*GP*CP*TP*GP*(CBR)P*AP*A)-3')

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

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

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


Theoretical massNumber of molelcules
Total (without water)13,6884
Polymers13,6884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_454-x-1/2,y,-z-1/41
crystal symmetry operation11_564-y+1/2,x+1,z-1/41
crystal symmetry operation15_465y-1,x+1,-z1
Buried area4100 Å2
ΔGint-3 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.520, 51.520, 111.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-105-

HOH

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Components

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


Mass: 3422.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 15% MPD, 120 mM calcium chloride, 20 mM lithium chloride, 8 mM spermidine, 30 mM sodium cacodylate; Equilibrated against 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9187 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9187 Å / Relative weight: 1
ReflectionResolution: 2.6→55.8 Å / Num. obs: 2540 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.743 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.058 / Rrim(I) all: 0.182 / Net I/σ(I): 11.5 / Num. measured all: 30879 / Scaling rejects: 36
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.82 / Num. measured all: 3740 / Num. unique obs: 294 / CC1/2: 0.233 / Rpim(I) all: 0.526 / Rrim(I) all: 1.895 / Net I/σ(I) obs: 1.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→46.78 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.822 / SU B: 17.568 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.71 / ESU R Free: 0.404
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3165 254 10.1 %RANDOM
Rwork0.2665 ---
obs0.2727 2272 100 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 94.19 Å2 / Biso mean: 46.873 Å2 / Biso min: 17.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2--0.05 Å20 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 2.6→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 446 0 7 453
Biso mean---38.81 -
Num. residues----22
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011500
X-RAY DIFFRACTIONr_bond_other_d0.0030.02244
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.303768
X-RAY DIFFRACTIONr_angle_other_deg1.6273576
X-RAY DIFFRACTIONr_chiral_restr0.0930.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02122
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 16 -
Rwork0.446 168 -
all-184 -
obs--100 %

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