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- PDB-3v06: Crystal structure of S-6'-Me-3'-fluoro hexitol nucleic acid -

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Basic information

Entry
Database: PDB / ID: 3v06
TitleCrystal structure of S-6'-Me-3'-fluoro hexitol nucleic acid
ComponentsDNA (5'-D(*GP*CP*GP*TP*AP*(F5H)P*AP*CP*GP*C)-3')
KeywordsDNA / A-form DNA / 3'-fluoro hexitol nucleic acid / FHNA / S-6'-Me-FHNA / antisense oligonucleotides
Function / homologySTRONTIUM ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Biochemistry / Year: 2012
Title: Insights from crystal structures into the opposite effects on RNA affinity caused by the s- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic Acid.
Authors: Pallan, P.S. / Yu, J. / Allerson, C.R. / Swayze, E.E. / Seth, P. / Egli, M.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _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*(F5H)P*AP*CP*GP*C)-3')
B: DNA (5'-D(*GP*CP*GP*TP*AP*(F5H)P*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2703
Polymers6,1822
Non-polymers881
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-32 kcal/mol
Surface area3670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.879, 45.222, 46.598
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*(F5H)P*AP*CP*GP*C)-3')


Mass: 3091.049 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SR / STRONTIUM ION / Strontium


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40 mM sodium cacodylate, 40 mM lithium chloride, 80 mM strontium chloride, 20 mM magnesium chloride, 12 mM spermine tetrahydrochloride, 10% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.53→32.45 Å / Num. all: 8268 / Num. obs: 8157 / % possible obs: 98.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 46.3
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 5.7 / % possible all: 70.2

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Processing

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

3ey2


Resolution: 1.53→32.45 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.963 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.1 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22693 377 4.6 %RANDOM
Rwork0.16715 ---
obs0.16997 7780 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---1 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.53→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 1 77 488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021460
X-RAY DIFFRACTIONr_angle_refined_deg2.4932.972714
X-RAY DIFFRACTIONr_chiral_restr0.1150.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02210
X-RAY DIFFRACTIONr_scbond_it3.5883458
X-RAY DIFFRACTIONr_scangle_it4.4224.5704
X-RAY DIFFRACTIONr_rigid_bond_restr2.7243458
LS refinement shellResolution: 1.53→1.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 19 -
Rwork0.167 414 -
obs--70.18 %

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