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- PDB-3sd8: Crystal structure of Ara-FHNA decamer DNA -

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Basic information

Entry
Database: PDB / ID: 3sd8
TitleCrystal structure of Ara-FHNA decamer DNA
Components5'-D(*GP*CP*GP*TP*AP*(F4H)P*AP*CP*GP*C)-3'
KeywordsDNA / A-form DNA / Ara-3'-fluoro hexitol nucleic acid / Ara-FHNA / antisense oligonucleotides
Function / homologySTRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsEgli, M. / Pallan, P.S.
CitationJournal: To be Published
Title: Structural Origins of Opposite Effects on Stability by Axial and Equatorial 3'-Fluoro Modifications of Hexitol Nucleic Acid (HNA)
Authors: Egli, M. / Pallan, P.S. / Allerson, C.R. / Prakash, T.P. / Berdeja, A. / Yu, J. / Bhat, B. / Swayze, E.E. / Seth, P.
History
DepositionJun 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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

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Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*TP*AP*(F4H)P*AP*CP*GP*C)-3'
B: 5'-D(*GP*CP*GP*TP*AP*(F4H)P*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2423
Polymers6,1542
Non-polymers881
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-29 kcal/mol
Surface area3700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.003, 42.855, 45.833
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 5'-D(*GP*CP*GP*TP*AP*(F4H)P*AP*CP*GP*C)-3'


Mass: 3077.023 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Ara-3'-fluoro hexitol (Ara-FHNA) modified DNA decamer
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1uL 1.5 mM DNA + 1 uL 40 mM sodium cacodylate, pH 6.0, 80 mM strontium chloride, 12mM spermine tetrahydrochloride, 10% MPD were equilibrated against a reservoir of 1 mL 35% MPD, VAPOR ...Details: 1uL 1.5 mM DNA + 1 uL 40 mM sodium cacodylate, pH 6.0, 80 mM strontium chloride, 12mM spermine tetrahydrochloride, 10% MPD were equilibrated against a reservoir of 1 mL 35% MPD, 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: 0.769
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.769 Å / Relative weight: 1
ReflectionResolution: 1.67→32 Å / Num. all: 6288 / Num. obs: 6138 / % possible obs: 97.59 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 54.1
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
CCP4MOLREPmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EY2

3ey2


Resolution: 1.67→31.3 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.459 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 516 7.8 %RANDOM
Rwork0.19071 ---
obs0.19456 6138 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.377 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---1.16 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.67→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 1 29 438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021454
X-RAY DIFFRACTIONr_angle_refined_deg1.7383690
X-RAY DIFFRACTIONr_chiral_restr0.1050.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02210
X-RAY DIFFRACTIONr_scbond_it4.7823454
X-RAY DIFFRACTIONr_scangle_it6.0634.5690
X-RAY DIFFRACTIONr_rigid_bond_restr3.4353454
LS refinement shellResolution: 1.668→1.712 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 45 -
Rwork0.226 438 -
obs--95.45 %

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