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

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Basic information

Entry
Database: PDB / ID: 2dqq
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
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.3Feb 17, 2021Group: Derived calculations / Source and taxonomy / Category: pdbx_entity_src_syn / struct_conn / struct_site
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _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_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
Revision 1.4Oct 25, 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

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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)5,9674
Polymers5,6472
Non-polymers3202
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.471, 52.471, 42.488
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#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 / Source: (synth.) synthetic construct (others)
#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 / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CMY / (6-AMINOHEXYL)CARBAMIC ACID


Mass: 160.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25mM sodium cacodylate, pH 7.0, 5mM spermine tetrahydrochloride, 25mM lithium chloride and 7.5% MPD, equilibrated against 35% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2spermine tetrahydrochloride11
3lithium chloride11
4MPD11
5HOH11
6sodium cacodylate12
7lithium 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: Dec 12, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.488 Å / Num. obs: 4587 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.5 / % 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→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
Rfree0.2844 469 -RANDOM
Rwork0.2463 ---
all-4538 --
obs-4494 99 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.241 Å2-6.598 Å20 Å2
2--3.241 Å20 Å2
3----6.482 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 374 20 62 456

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