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- PDB-2qs6: Structure of a Hoogsteen antiparallel duplex with extra-helical t... -

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Entry
Database: PDB / ID: 2qs6
TitleStructure of a Hoogsteen antiparallel duplex with extra-helical thymines
ComponentsDNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
KeywordsDNA / Hoogsteen / Oligonucleotide / Thymines
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsPous, J. / Urpi, L. / Subirana, J.A. / Gouyette, C. / Navaza, J. / Campos, J.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs.
Authors: Pous, J. / Urpi, L. / Subirana, J.A. / Gouyette, C. / Navaza, J. / Campos, J.L.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
B: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
C: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
D: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
E: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
F: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
G: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
H: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
I: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
J: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
K: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
L: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
M: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
N: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)33,60914
Polymers33,60914
Non-polymers00
Water72140
1
A: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
B: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-3.4 kcal/mol
Surface area2990 Å2
MethodPISA
2
C: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
D: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-2.4 kcal/mol
Surface area2940 Å2
MethodPISA
3
E: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
F: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-3.6 kcal/mol
Surface area2960 Å2
MethodPISA
4
G: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
H: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-1.9 kcal/mol
Surface area2930 Å2
MethodPISA
5
I: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
J: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-2.5 kcal/mol
Surface area2800 Å2
MethodPISA
6
K: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
L: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-2.9 kcal/mol
Surface area2910 Å2
MethodPISA
7
M: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')
N: DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Theoretical massNumber of molelcules
Total (without water)4,8012
Polymers4,8012
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-1.8 kcal/mol
Surface area2840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.836, 39.540, 71.753
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain
DNA (5'-D(*DAP*DTP*DAP*DTP*DAP*DTP*DCP*DT)-3')


Mass: 2400.616 Da / Num. of mol.: 14 / Source method: obtained synthetically / Details: Phosphoramidite method
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drop: 1.0mM octamer, 10% MPD, 22mM sodium cacodylate, 10mM magnesium chloride, 1.5mM spermine tetrachloride. Reservoir: from 25% to 45% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
10% MPD11
2sodium cacodylate11
3magnesium chloride11
4spermine tetrachloride11
525% to 45% MPD12

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Data collection

DiffractionMean temperature: 113.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2004
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.08→71.43 Å / Num. all: 6262 / Num. obs: 6262 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.35 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.5
Reflection shellResolution: 3.08→3.21 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.6 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D(ATATAT)2 model with Hoogsteen base pairs (from NDB entry UD0049)

Resolution: 3.08→71.43 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.895 / SU B: 59.211 / SU ML: 0.506 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.629 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 555 9.7 %RANDOM
Rwork0.20689 ---
obs0.21446 5188 88.86 %-
all-6503 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 65.775 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å2-4.62 Å2
2---1.18 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 3.08→71.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2181 0 40 2221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0850.0552613
X-RAY DIFFRACTIONr_bond_other_d0.0020.021164
X-RAY DIFFRACTIONr_angle_refined_deg1.0733716
X-RAY DIFFRACTIONr_angle_other_deg0.93932863
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_restr0.0610.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.250.2908
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.4040.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1120.210
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.22
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_scbond_it1.18432613
X-RAY DIFFRACTIONr_scangle_it1.6684.53716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.08→3.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 31 -
Rwork0.265 251 -
obs--58.02 %
Refinement TLS params.Method: refined / Origin x: 77.622 Å / Origin y: 6.414 Å / Origin z: 42.449 Å
111213212223313233
T-0.1341 Å20.1767 Å20.1262 Å2-0.0274 Å20.2242 Å2---0.1792 Å2
L2.0275 °2-2.5723 °22.1497 °2-5.8677 °2-4.1624 °2--3.3643 °2
S-0.0876 Å °-0.1444 Å °-0.0793 Å °0.0177 Å °0.3001 Å °0.3277 Å °0.0091 Å °-0.212 Å °-0.2125 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 61 - 6
2X-RAY DIFFRACTION1BB1 - 61 - 6
3X-RAY DIFFRACTION1CC1 - 61 - 6
4X-RAY DIFFRACTION1DD1 - 61 - 6
5X-RAY DIFFRACTION1EE1 - 61 - 6
6X-RAY DIFFRACTION1FF1 - 61 - 6
7X-RAY DIFFRACTION1GG1 - 61 - 6
8X-RAY DIFFRACTION1HH1 - 61 - 6
9X-RAY DIFFRACTION1II1 - 61 - 6
10X-RAY DIFFRACTION1JJ1 - 61 - 6
11X-RAY DIFFRACTION1KK1 - 61 - 6
12X-RAY DIFFRACTION1LL1 - 61 - 6
13X-RAY DIFFRACTION1MM1 - 61 - 6
14X-RAY DIFFRACTION1NN1 - 61 - 6

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