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- PDB-3hcl: Helical superstructures in a DNA oligonucleotide crystal -

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Basic information

Entry
Database: PDB / ID: 3hcl
TitleHelical superstructures in a DNA oligonucleotide crystal
ComponentsDNA (5'-D(*CP*GP*AP*TP*AP*T)-3')
KeywordsDNA / oligonucleotide / superhelices / supramolecular chemistry
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDe Luchi, D. / Martinez de Ilarduya, I. / Subirana, J.A. / Uson, I. / Campos, J.L.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: A geometric approach to the crystallographic solution of nonconventional DNA structures: helical superstructures of d(CGATAT)
Authors: Martinez de Ilarduya, I. / De Luchi, D. / Subirana, J.A. / Campos, J.L. / Uson, I.
History
DepositionMay 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*AP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)1,8081
Polymers1,8081
Non-polymers00
Water362
1
A: DNA (5'-D(*CP*GP*AP*TP*AP*T)-3')

A: DNA (5'-D(*CP*GP*AP*TP*AP*T)-3')

A: DNA (5'-D(*CP*GP*AP*TP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,4253
Polymers5,4253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
crystal symmetry operation12_566x,x-y+1,-z+4/31
Unit cell
Length a, b, c (Å)38.326, 38.326, 56.821
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
DetailsThe ATAT part of the structure forms a B-DNA structure by the symmetry operation: x-y,-y+1,-z. The CG part of the sequence forms a Z-DNA step by the symmetry operation: x,x-y,-z+1/3. The cgatat sequence pairs itself with various symmetry equivalents leading to a complex interconnected superstructure.

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Components

#1: DNA chain DNA (5'-D(*CP*GP*AP*TP*AP*T)-3')


Mass: 1808.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.33 Å3/Da / Density % sol: 63.08 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9783 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2.59→35 Å / Num. all: 924 / Num. obs: 924 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 0.99 % / Biso Wilson estimate: 80 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.017 / Net I/σ(I): 43.8
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 1 % / Mean I/σ(I) obs: 12.5 / Num. unique all: 56 / Rsym value: 0.071 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPVERSION 10.2.6phasing
REFMAC5.5.0046refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 231D

231d


Resolution: 2.59→33.19 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 11.662 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27509 52 5.6 %RANDOM
Rwork0.23653 ---
obs0.23862 869 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.871 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.63 Å20 Å2
2--1.26 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.59→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 0 2 122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021134
X-RAY DIFFRACTIONr_angle_refined_deg2.6613205
X-RAY DIFFRACTIONr_chiral_restr0.0990.223
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0263
X-RAY DIFFRACTIONr_scbond_it1.9493134
X-RAY DIFFRACTIONr_scangle_it2.9714.5205
LS refinement shellResolution: 2.586→2.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.72 2 -
Rwork0.586 60 -
obs--100 %

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