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- PDB-1xuw: Structural rationalization of a large difference in RNA affinity ... -

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Basic information

Entry
Database: PDB / ID: 1xuw
TitleStructural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogs
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(NMT)P*AP*CP*GP*C)-3')
KeywordsDNA / RNA mimetic methylcarbamate amide analog
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsPattanayek, R. / Sethaphong, L. / Pan, C. / Prhavc, M. / Prakash, T.P. / Manoharan, M. / Egli, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Structural rationalization of a large difference in RNA affinity despite a small difference in chemistry between two 2'-O-modified nucleic acid analogues.
Authors: Pattanayek, R. / Sethaphong, L. / Pan, C. / Prhavc, M. / Prakash, T.P. / Manoharan, M. / Egli, M.
History
DepositionOct 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 (5'-D(*GP*CP*GP*TP*AP*(NMT)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(NMT)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2402
Polymers6,2402
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.599, 44.876, 46.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDecamer duplex

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Components

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


Mass: 3120.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetically created
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 4 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM 10mer, 40mM sodium cacodylate, 12 mM spermine 4HCl, 80mM potassium chloride, 10% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.96297 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96297 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. all: 14402 / Num. obs: 14402 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.254 / Num. unique all: 1389 / % possible all: 96

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
MAR345data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPL

1dpl


Resolution: 1.25→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.221 711 RANDOM
Rwork0.153 --
all0.153 13637 -
obs0.153 13637 -
Refinement stepCycle: LAST / Resolution: 1.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 416 0 153 569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.02

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