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- PDB-3oz5: S-Methyl Carbocyclic LNA -

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Basic information

Entry
Database: PDB / ID: 3oz5
TitleS-Methyl Carbocyclic LNA
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3')
KeywordsDNA / A-form DNA / S-Methyl carbocyclic LNA / S-Me-c-LNA / antisense oligonucleotides / S-Methyl-carbocyclic LNA
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsSeth, P.R. / Allerson, C.A. / Berdeja, A. / Siwkowski, A. / Pallan, P.S. / Gaus, H. / Prakash, T.P. / Watt, A.T. / Egli, M. / Swayze, E.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA.
Authors: Seth, P.P. / Allerson, C.R. / Berdeja, A. / Siwkowski, A. / Pallan, P.S. / Gaus, H. / Prakash, T.P. / Watt, A.T. / Egli, M. / Swayze, E.E.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*(UMX)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(UMX)P*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3443
Polymers6,1422
Non-polymers2021
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-2 kcal/mol
Surface area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.465, 44.112, 45.954
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*(UMX)P*AP*CP*GP*C)-3')


Mass: 3071.043 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.02 Å3/Da / Density % sol: 39.07 %
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
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2sodium chloride11
3potassium chloride11
4spermine tetrahydrochloride11
5MPD11
6sodium cacodylate12
7sodium chloride12
8potassium chloride12
9spermine tetrahydrochloride12
10MPD12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0079 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0079 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 11265 / Num. obs: 11119 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.7 / Num. unique all: 999 / % possible all: 91.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EY2

3ey2


Resolution: 1.36→31.82 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.736 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18587 857 7.7 %RANDOM
Rwork0.14575 ---
obs0.14888 10229 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.36→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 8 78 494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021461
X-RAY DIFFRACTIONr_angle_refined_deg2.3983698
X-RAY DIFFRACTIONr_chiral_restr0.1830.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02208
X-RAY DIFFRACTIONr_scbond_it3.0593461
X-RAY DIFFRACTIONr_scangle_it3.7244.5698
X-RAY DIFFRACTIONr_rigid_bond_restr2.4243461
LS refinement shellResolution: 1.36→1.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 56 -
Rwork0.28 601 -
obs--81.51 %

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