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- PDB-3uke: (S)-cMOE-BNA decamer structure -

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Basic information

Entry
Database: PDB / ID: 3uke
Title(S)-cMOE-BNA decamer structure
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(CSM)P*AP*CP*GP*C)-3')
KeywordsDNA / A-FORM DNA / BICYCLIC NUCLEIC ACID / BNA / c-MOE-BNA / ANTISENSE OLIGONUCLEOTIDES
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLREP, (CCP4) / Resolution: 1.68 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Chem.Commun.(Camb.) / Year: 2012
Title: Structure and nuclease resistance of 2',4'-constrained 2'-O-methoxyethyl (cMOE) and 2'-O-ethyl (cEt) modified DNAs.
Authors: Pallan, P.S. / Allerson, C.R. / Berdeja, A. / Seth, P.P. / Swayze, E.E. / Prakash, T.P. / Egli, M.
History
DepositionNov 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*GP*TP*AP*(CSM)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(CSM)P*AP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2062
Polymers6,2062
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-2 kcal/mol
Surface area3860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.492, 44.660, 46.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3103.042 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM sodium cacodylate, 6 mM sodium chloride, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.007 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 6270 / Num. obs: 6236 / % possible obs: 99.45 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 29.6
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.41 / Num. unique all: 612 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MD2diffractometer software (with LS-CAT developed extensions)data collection
CCP4model building
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLREP, (CCP4)
Starting model: PDB entry 3EY2

3ey2


Resolution: 1.68→32.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.22 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24979 606 9.7 %RANDOM
Rwork0.18103 ---
obs0.18833 5630 99.54 %-
all-6236 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.174 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--1.41 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.68→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 412 0 53 465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021462
X-RAY DIFFRACTIONr_angle_refined_deg2.3142.989710
X-RAY DIFFRACTIONr_chiral_restr0.1310.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0290.02208
X-RAY DIFFRACTIONr_scbond_it4.6033462
X-RAY DIFFRACTIONr_scangle_it5.2384.5708
X-RAY DIFFRACTIONr_rigid_bond_restr3.5753462
LS refinement shellResolution: 1.68→1.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 36 -
Rwork0.199 390 -
obs-390 94.04 %

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