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- PDB-4u9m: Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds -

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Basic information

Entry
Database: PDB / ID: 4u9m
TitleStructure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds
ComponentsDNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
KeywordsDNA
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsAcosta-Reyes, F.J. / Alechaga, E. / Subirana, J.A. / Campos, J.L.
Funding support Spain, Mexico, 3items
OrganizationGrant numberCountry
Feder funds and the Ministerio de Ciencia e InovacionBFU-2009-10380 Spain
Generalitat de CatalunyaSRG2009-1208 Spain
CONACYTReg. 212993 Mexico
CitationJournal: Plos One / Year: 2015
Title: Structure of the DNA Duplex d(ATTAAT)2 with Hoogsteen Hydrogen Bonds.
Authors: Acosta-Reyes, F.J. / Alechaga, E. / Subirana, J.A. / Campos, J.L.
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
B: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
C: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
E: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)9,0365
Polymers9,0365
Non-polymers00
Water00
1
A: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
B: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,6142
Polymers3,6142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-6 kcal/mol
Surface area2370 Å2
MethodPISA
2
C: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')
D: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,6142
Polymers3,6142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-6 kcal/mol
Surface area2370 Å2
MethodPISA
3
E: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')

E: DNA (5'-D(*AP*TP*TP*AP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,6142
Polymers3,6142
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area540 Å2
ΔGint-6 kcal/mol
Surface area2430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.756, 42.898, 99.422
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 1807.241 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 286 K / Method: vapor diffusion / pH: 6.5
Details: 0.8mM of the oligonucleotide, 20mM sodium cacodylate buffer (pH = 6.5), 3mM spermine, 100mM N-ethylaniline hydrochloride and 5% MPD, equilibrated against a reservoir with 30% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9762 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2005
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.184
111/2H+1/2K, -3/2H+1/2K, L20.156
111/2H-1/2K, 3/2H+1/2K, L30.147
11-h,-k,l40.168
11-1/2H+1/2K, -3/2H-1/2K, L50.185
11-1/2H-1/2K, 3/2H-1/2K, L60.159
ReflectionResolution: 3.13→33.14 Å / Num. obs: 1888 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 144 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.48
Reflection shellResolution: 3.13→3.241 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.88 / % possible all: 99.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: helical parameters taken from 2qs6, 1rsb

2qs6

1rsb


Resolution: 3.13→33.14 Å / Cor.coef. Fo:Fc: 0.991 / Cor.coef. Fo:Fc free: 0.973 / SU B: 24.326 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19979 107 5.7 %RANDOM
Rwork0.14582 ---
obs0.1481 1773 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 138.561 Å2
Baniso -1Baniso -2Baniso -3
1--9.92 Å20 Å293.61 Å2
2--41.24 Å20 Å2
3----31.32 Å2
Refinement stepCycle: 1 / Resolution: 3.13→33.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 600 0 0 600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.011670
X-RAY DIFFRACTIONr_bond_other_d0.0230.02350
X-RAY DIFFRACTIONr_angle_refined_deg0.9391.1781025
X-RAY DIFFRACTIONr_angle_other_deg6.6783830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it16.5514.236668
X-RAY DIFFRACTIONr_scbond_other16.54214.241667
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other24.34521.3521024
X-RAY DIFFRACTIONr_long_range_B_refined26.7122892
X-RAY DIFFRACTIONr_long_range_B_other26.7172891
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.129→3.21 Å /
Num. reflection% reflection
Rwork116 -
obs-96.83 %

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