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- PDB-2dpb: Crystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)c... -

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Basic information

Entry
Database: PDB / ID: 2dpb
TitleCrystal Structure of d(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine
ComponentsDNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3')
KeywordsDNA / modified nucleotide / 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine / B-DNA
Function / homology(6-AMINOHEXYL)CARBAMIC ACID / : / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsJuan, E.C.M. / Kondo, J. / Kurihara, T. / Ito, T. / Ueno, Y. / Matsuda, A. / Takenaka, A.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules
Authors: Juan, E.C.M. / Kondo, J. / Kurihara, T. / Ito, T. / Ueno, Y. / Matsuda, A. / Takenaka, A.
History
DepositionMay 8, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3')
B: DNA (5'-D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6585
Polymers7,2992
Non-polymers3603
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.539, 40.833, 64.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3649.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This DNA dodecamer is a synthetic construct.
#2: Chemical ChemComp-CMY / (6-AMINOHEXYL)CARBAMIC ACID


Mass: 160.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O2
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20mM sodium cacodylate, pH 6.0, 40mM potassium chloride, 6mM spermine tetrahydrochloride and 5%(v/v) MPD, equilibrated against 35% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2potassium chloride11
3spermine tetrahydrochloride11
4MPD11
5HOH11
6sodium cacodylate12
7potassium chloride12
8MPD12
9HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→19.463 Å / Num. obs: 11296 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.044 / Net I/σ(I): 7.4
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 355D

355d


Resolution: 1.5→10 Å / σ(F): 3 / Stereochemistry target values: Maximum Likelihood
Details: The value of the item "Number reflections (observed)" is the number of reflections used in refinement. This value excludes the reflections that have sigma(F) less than 3.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1136 -RANDOM
Rwork0.1934 ---
all-11265 --
obs-10951 97.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.466 Å20 Å20 Å2
2---1.774 Å20 Å2
3---3.239 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 21 236 741

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