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- PDB-7sb8: d(GA(CGA)5) parallel-stranded homo-duplex -

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Basic information

Entry
Database: PDB / ID: 7sb8
Titled(GA(CGA)5) parallel-stranded homo-duplex
ComponentsGA(CGA)5
KeywordsDNA / triplet repeat DNA / parallel-stranded duplex / non-canonical DNA / d(CGA)
Function / homologyCOBALT HEXAMMINE(III) / STRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.317 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
DepositionSep 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 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

Downloads & links

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Assembly

Deposited unit
A: GA(CGA)5
B: GA(CGA)5
D: GA(CGA)5
E: GA(CGA)5
F: GA(CGA)5
C: GA(CGA)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,66126
Polymers31,5336
Non-polymers2,12920
Water8,269459
1
A: GA(CGA)5
B: GA(CGA)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,29410
Polymers10,5112
Non-polymers7838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: GA(CGA)5
C: GA(CGA)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3459
Polymers10,5112
Non-polymers8347
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: GA(CGA)5
F: GA(CGA)5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0227
Polymers10,5112
Non-polymers5125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.677, 30.422, 180.822
Angle α, β, γ (deg.)90.000, 90.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
GA(CGA)5


Mass: 5255.427 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CoH18N6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 1.72 Å3/Da / Density % sol: 28.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 8% PEG400, 96 mM strontium chloride, 32 mM lithium chloride, 8 mM hexamminecobalt(III) chloride, 24 mM sodium cacodylate, equilibrated against 30% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.317→90.41 Å / Num. obs: 48232 / % possible obs: 94.7 % / Redundancy: 4.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.049 / Rrim(I) all: 0.106 / Net I/σ(I): 9.9
Reflection shellResolution: 1.317→1.34 Å / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2 / Num. unique obs: 2175 / CC1/2: 0.82 / Rpim(I) all: 0.35 / Rrim(I) all: 0.757

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1ixj


Resolution: 1.317→90.409 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2139 2311 4.81 %
Rwork0.1713 45701 -
obs0.1734 48012 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 233.18 Å2 / Biso mean: 19.4304 Å2 / Biso min: 3.7 Å2
Refinement stepCycle: final / Resolution: 1.317→90.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2100 299 479 2878
Biso mean--43.08 27.77 -
Num. residues----102
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.317-1.34380.2922990.1913241585
1.3438-1.37310.24211160.1957252590
1.3731-1.4050.3002960.2023270792
1.405-1.44010.26131330.1892256592
1.4401-1.47910.24911320.1728261392
1.4791-1.52260.24841400.1683277194
1.5226-1.57180.19861300.1525259394
1.5718-1.62790.21861640.1415269695
1.6279-1.69310.22941580.1522265695
1.6931-1.77020.22521710.15271295
1.7702-1.86350.23241420.1577265595
1.8635-1.98030.16371330.1601279195
1.9803-2.13320.20671230.1533279697
2.1332-2.34790.19531300.1646276797
2.3479-2.68760.25291310.203280797
2.6876-3.38620.20921570.1908279595
3.3862-90.4090.19431560.1675283795

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