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- PDB-3fx8: Distinct recognition of three-way DNA junctions by a thioester va... -

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Basic information

Entry
Database: PDB / ID: 3fx8
TitleDistinct recognition of three-way DNA junctions by a thioester variant of a metallo-supramolecular cylinder ('helicate')
Components(5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / Self-assembly / DNA-based nanomaterial
Function / homologyChem-5PM / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.44 Å
AuthorsBoer, D.R. / Uson, I. / Coll, M.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders.
Authors: Boer, D.R. / Kerckhoffs, J.M. / Parajo, Y. / Pascu, M. / Uson, I. / Lincoln, P. / Hannon, M.J. / Coll, M.
#1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: Molecular recognition of a three-way DNA junction by a metallosupramolecular helicate.
Authors: Oleksy, A. / Blanco, A.G. / Boer, R. / Uson, I. / Aymami, J. / Rodger, A. / Hannon, M.J. / Coll, M.
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: (5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8227
Polymers1,8091
Non-polymers1,0126
Water00
1
C: (5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

C: (5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

C: (5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,46521
Polymers5,4283
Non-polymers3,03718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_467z-1/2,-x+3/2,-y+21
crystal symmetry operation12_675-y+3/2,-z+2,x+1/21
Buried area4580 Å2
ΔGint-68.9 kcal/mol
Surface area2430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.249, 49.249, 49.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11C-101-

FE2

21C-102-

FE2

31C-201-

FE2

41C-202-

FE2

DetailsA THREE-WAY JUNCTION (CHAINS A AND C) WITH DISCONTINUOUS DNA STRANDS CAN BE GENERATED THROUGH THE FOLLOWING TRANSFORMATIONS ON CHAIN C: [Z+1/2,-X+1/2,-Y+(0 1 1)], [Y+1/2,-Z+1/2,-X+(-1 1 1)], [-X, Y+1/2,-Z+1/2+(0 1 0)], [-Z,X+1/2,-Y+1/2+(0 1 1)], [Y,Z,X+(0 2 1)] AND THE FOLLOWING TRANSFORMATIONS ON CHAIN A: [-Z,X+1/2,-Y+1/2 +(0 1 1)], [Y+1/2,-Z+1/2,-X +(-1 1 1)]

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Components

#1: DNA chain (5'-D(*CP*GP*TP*AP*CP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic hexanucleotide. The sequence is palindromic
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-5PM / 4,4'-sulfanediylbis{N-[(1E)-pyridin-2-ylmethylidene]aniline} / 1,1-Bis(N-(4-phenyl)-2-pyridylcarboxaldimine)thioether


Mass: 394.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H18N4S
Nonpolymer detailsLIGAND 5PM C 111 WITH TWO IRON ATOMS FE2 C 101 AND C 102 IS THE M HELICAL ENANTIOMER OF [FE2L3], ...LIGAND 5PM C 111 WITH TWO IRON ATOMS FE2 C 101 AND C 102 IS THE M HELICAL ENANTIOMER OF [FE2L3], WHERE L IS 4,4'-SULFANEDIYLBIS{N-[(1E)-PYRIDIN-2-YLMETHYLIDENE]ANILINE}

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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: 5.5 Å3/Da / Density % sol: 77.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1 microliter of 10 mM cylinder, 1 microliter of 3 mM DNA, 2 microliters of crystallization buffer (10 mM Magnesium chloride, 5% v/v Isopropanol, 50 mM Tris-HCl), pH 8.5, VAPOR DIFFUSION, ...Details: 1 microliter of 10 mM cylinder, 1 microliter of 3 mM DNA, 2 microliters of crystallization buffer (10 mM Magnesium chloride, 5% v/v Isopropanol, 50 mM Tris-HCl), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium chloride11
2Isopropanol11
3Tris-HCl11
4Magnesium chloride12
5Isopropanol12
6Tris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7366, 1.7410, 1.7311
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2006
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.73661
21.7411
31.73111
ReflectionResolution: 2.44→24.63 Å / Num. all: 1573 / Num. obs: 1573 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 94 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 36.1
Reflection shellResolution: 2.44→2.58 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.2 / Num. unique all: 228 / % possible all: 100

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Processing

Software
NameClassification
ProDCdata collection
SHELXDEphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.44→24.63 Å / Isotropic thermal model: isotropic
RfactorNum. reflection% reflectionSelection details
Rfree0.212 74 -Random
Rwork0.187 ---
all0.187 1573 --
obs0.187 1540 98 %-
Solvent computationSolvent model: BABINET (SHELXL SWAT)
Displacement parametersBiso mean: 79.4 Å2
Refinement stepCycle: LAST / Resolution: 2.44→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 62 0 182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.005
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.006
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_from_restr_planes0.031
LS refinement shellResolution: 2.44→2.55 Å /
RfactorNum. reflection
Rwork0.358 -
obs-165

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