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- PDB-2dqo: Crystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-am... -

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Basic information

Entry
Database: PDB / ID: 2dqo
TitleCrystal Structure of d(CXCTXCTTC):r(gaagaagag) Where X is 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine
Components
  • DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3')
  • RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
KeywordsDNA-RNA HYBRID / modified nucleotide / 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine / A-form RNA:DNA hybrid duplex
Function / homology: / (6-AMINOHEXYL)CARBAMIC ACID / DNA / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJuan, E.C.M. / Kondo, J. / 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 29, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3')
B: RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3119
Polymers5,6472
Non-polymers6647
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.400, 51.400, 44.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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DNA chain / RNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3')


Mass: 2664.734 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic constructs
#2: RNA chain RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3')


Mass: 2981.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic constructs

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Non-polymers , 4 types, 73 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CMY / (6-AMINOHEXYL)CARBAMIC ACID


Mass: 160.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O2
#5: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25mM sodium cacodylate, pH 7.0, 5mM spermine tetrahydrochloride, 50mM sodium chloride, 50mM barium chloride and 5% MPD, equilibrated against 35% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2spermine tetrahydrochloride11
3sodium chloride11
4barium chloride11
5MPD11
6HOH11
7sodium cacodylate12
8sodium chloride12
9barium chloride12
10MPD12
11HOH12

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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: Oct 26, 2002
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→31.365 Å / Num. obs: 3021 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.059 / Net I/σ(I): 8.3
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 479D

479d


Resolution: 2.3→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
Rfree0.2757 282 -RANDOM
Rwork0.2161 ---
all-2987 --
obs-2963 99.2 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.224 Å2-13.753 Å20 Å2
2---0.224 Å20 Å2
3---0.447 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 25 66 465

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