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- PDB-1rsb: X-ray study of the DNA oligomer d(ATATAT) in P65 space group -

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Basic information

Entry
Database: PDB / ID: 1rsb
TitleX-ray study of the DNA oligomer d(ATATAT) in P65 space group
Components5'-D(*AP*TP*AP*TP*AP*T)-3'
KeywordsDNA / Antiparallel Hoogsteen DNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsAbrescia, N.G. / Gonzalez, C. / Gouyette, C. / Subirana, J.A.
Citation
Journal: Biochemistry / Year: 2004
Title: X-ray and NMR studies of the DNA oligomer d(ATATAT): Hoogsteen base pairing in duplex DNA.
Authors: Abrescia, N.G. / Gonzalez, C. / Gouyette, C. / Subirana, J.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing
Authors: Abrescia, N.G.A. / Thompson, A. / Huynh-Dinh, T. / Subirana, J.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: When pseudosymmetry and merohedral twinning came across: thecase of the d(ATATAT) oligonucleotide in a hexagonal lattice
Authors: Abrescia, N.G.A. / Subirana, J.A.
#3: Journal: J.Am.Chem.Soc. / Year: 2003
Title: Theoretical Study of a New DNA structure: The antiparallel Hoogsteen Duplex
Authors: Cubero, E. / Abrescia, N.G.A. / Subirana, J.A. / Luque, J.F. / Orozco, M.
History
DepositionDec 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,2294
Polymers7,2294
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.313, 32.313, 117.779
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 1807.241 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The self-complementary hexamer d(ATATAT) was synthetized on automatic synthesizer by the phosphoramidite method and purified by gel filtration and reverse phase HPLC.
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.87 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Spermine, NaCl,MPD,cacodylate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 286K
Components of the solutions
IDNameCrystal-IDSol-ID
1Spermine11
2NaCl11
3MPD11
4cacodylate11
5H2O11
6MPD12
7cacodylate12
8H2O12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.17→20 Å / Num. all: 3712 / Num. obs: 3693 / % possible obs: 98.3 % / Redundancy: 19.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 38.2
Reflection shellResolution: 2.17→2.22 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.1 / Num. unique all: 213 / % possible all: 97.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB entry UD0035

Resolution: 2.17→15 Å / Isotropic thermal model: Anistropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS top/param files / Details: Used target= twin_lsq (twinned crystal)
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 313 -RANDOM
Rwork0.2177 ---
all-3674 --
obs-3475 94.6 %-
Refinement stepCycle: LAST / Resolution: 2.17→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 442 0 34 476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006627
X-RAY DIFFRACTIONc_angle_deg1.19291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID
2.17-2.270.356340.449X-RAY DIFFRACTION
2.27-2.390.356400.449X-RAY DIFFRACTION

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