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- PDB-4f2x: Structure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer -

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Basic information

Entry
Database: PDB / ID: 4f2x
TitleStructure of 3'-Fluoro Cyclohexenyl Nucleic Acid Heptamer
Components
  • 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*(XTF)P*GP*CP*G)-3'
KeywordsDNA / Fluoro Cyclohexenyl Nucleic Acid / F-CeNA / Modified DNA / B-form DNA
Function / homologyCOBALT (III) ION / COBALT HEXAMMINE(III) / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 / 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*(XTF)P*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
C: 5'-D(*GP*CP*GP*(XTF)P*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,20812
Polymers8,5324
Non-polymers6768
Water1,38777
1
A: 5'-D(*GP*CP*GP*(XTF)P*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8248
Polymers4,2662
Non-polymers5586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-32 kcal/mol
Surface area3290 Å2
MethodPISA
2
C: 5'-D(*GP*CP*GP*(XTF)P*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3844
Polymers4,2662
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-15 kcal/mol
Surface area2900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.700, 33.862, 80.165
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*(XTF)P*GP*CP*G)-3'


Mass: 2182.451 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*AP*CP*GP*C)-3'


Mass: 2083.388 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical
ChemComp-3CO / COBALT (III) ION / Cobalt


Mass: 58.933 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Co
#5: 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: 42.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40 mM sodium cacodylate, 20 mM cobalt hexamine, 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: Feb 7, 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: 1.57→40.08 Å / Num. all: 10628 / Num. obs: 10592 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 38.6
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.63 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FL6

3fl6


Resolution: 1.57→40.08 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.219 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 507 4.8 %RANDOM
Rwork0.185 ---
all0.188 ---
obs-10085 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.805 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2--0.22 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 551 20 77 648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.00820.012627
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.505973
X-RAY DIFFRACTIONr_chiral_restr0.1150.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0270.02293
LS refinement shellResolution: 1.57→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 37 -
Rwork0.246 628 -
obs-507 97.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2943-0.6336-0.36721.06141.53363.0420.15480.1675-0.0846-0.0233-0.11170.05320.1373-0.2849-0.04310.0918-0.0054-0.00990.0980.00410.0806-6.5016-14.9637-12.1855
21.5734-0.3711.40240.1474-0.62144.6232-0.07730.05680.03440.03760.05680.0156-0.36510.21980.02040.1426-0.0292-0.00010.15680.01130.11033.8081-0.0155-8.1768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION1B1 - 7
3X-RAY DIFFRACTION2C1 - 7
4X-RAY DIFFRACTION2D1 - 7

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