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- PDB-4f2y: Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer -

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Basic information

Entry
Database: PDB / ID: 4f2y
TitleStructure of 3'-Fluoro Cyclohexenyl Nucleic Acid Decamer
Components5'-D(*GP*CP*GP*TP*AP*(XTF)P*AP*CP*GP*C)-3'
KeywordsDNA / Fluoro Cyclohexenyl Nucleic Acid / F-CeNA / Modified DNA / A-form DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: J.Org.Chem. / Year: 2012
Title: Synthesis and Antisense Properties of Fluoro Cyclohexenyl Nucleic Acid (F-CeNA), a Nuclease Stable Mimic of 2'-Fluoro RNA.
Authors: Seth, P.P. / Yu, J. / Jazayeri, A. / Pallan, P.S. / Allerson, C.R. / Ostergaard, M.E. / Liu, F. / Herdewijn, P. / Egli, M. / Swayze, E.E.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1954
Polymers6,1462
Non-polymers492
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area3800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.775, 38.299, 47.746
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*(XTF)P*AP*CP*GP*C)-3'


Mass: 3073.034 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.84 Å3/Da / Density % sol: 33.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40 mM sodium cacodylate, 20 mM cobalt hexamine, 40 mM lithium chloride, 20 mM magnesium chloride, 10% v/v MPD, pH 5.5, 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: Apr 6, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.59→29.875 Å / Num. all: 6450 / Num. obs: 6416 / % possible obs: 99.45 % / Observed criterion σ(I): 5 / Redundancy: 14.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 59.43
Reflection shellResolution: 1.59→1.66 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 9.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
CCP4model building
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EY2

3ey2


Resolution: 1.59→29.875 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.552 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(I): 5 / ESU R: 0.155 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25331 486 7.6 %RANDOM
Rwork0.18193 ---
obs0.18694 5930 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 2 52 462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.012456
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.517700
X-RAY DIFFRACTIONr_chiral_restr0.0770.264
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02218
X-RAY DIFFRACTIONr_rigid_bond_restr3.223456
X-RAY DIFFRACTIONr_sphericity_free22.969524
X-RAY DIFFRACTIONr_sphericity_bonded11.4615442
LS refinement shellResolution: 1.59→1.636 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 25 -
Rwork0.146 363 -
obs--94.87 %

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