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- PDB-5vxq: X-Ray crystallography structure of the parallel stranded duplex f... -

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Basic information

Entry
Database: PDB / ID: 5vxq
TitleX-Ray crystallography structure of the parallel stranded duplex formed by 5-rA5-dA-rA5
ComponentsDNA/RNA (5'-R(*AP*AP*AP*AP*A)-D(P*A)-R(P*AP*AP*AP*AP*A)-3')
KeywordsRNA / DNA / duplex
Function / homologyAMMONIUM ION / DNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.002 Å
AuthorsXie, J. / Chen, Y. / Wei, X. / Kozlov, G. / Gehring, K.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.
Authors: Copp, W. / Denisov, A.Y. / Xie, J. / Noronha, A.M. / Liczner, C. / Safaee, N. / Wilds, C.J. / Gehring, K.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: 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.title / _citation.year
Revision 1.2Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*AP*AP*AP*AP*A)-D(P*A)-R(P*AP*AP*AP*AP*A)-3')
B: DNA/RNA (5'-R(*AP*AP*AP*AP*A)-D(P*A)-R(P*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,44520
Polymers7,1212
Non-polymers32518
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint3 kcal/mol
Surface area2740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.799, 22.799, 164.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-228-

HOH

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-R(*AP*AP*AP*AP*A)-D(P*A)-R(P*AP*AP*AP*AP*A)-3')


Mass: 3560.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: modified RNA duplex / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.5 Å3/Da / Density % sol: 17.84 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 5
Details: 0.5 uL 5-rA5-dA-rA5 and RRM23 (98-269) in 10 mM HEPES, 100 mM sodium chloride, 2 mM DTT, pH 7.0 + 0.5 uL 1.6 M ammonium sulfate, 0.1 M citric acid, pH 5.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.28206 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 1, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28206 Å / Relative weight: 1
ReflectionResolution: 1.002→22.58 Å / Num. obs: 23843 / % possible obs: 96.4 % / Redundancy: 1 % / Net I/σ(I): 17.65
Reflection shellHighest resolution: 1.002 Å

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Processing

Software
NameVersionClassification
PHENIX1.9refinement
PHENIX1.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.002→22.58 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1598 --
Rwork0.1285 --
obs-23843 96.4 %
Refinement stepCycle: LAST / Resolution: 1.002→22.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 476 18 71 565

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