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- PDB-1dcv: B-DNA DECAMER WITH CENTRAL TA DINUCLEOTIDE -

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Basic information

Entry
Database: PDB / ID: 1dcv
TitleB-DNA DECAMER WITH CENTRAL TA DINUCLEOTIDE
ComponentsDNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
KeywordsDNA / CENTRAL TA DINUCLEOTIDE / DEOXYRIBONUCLEIC ACID
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEichman, B.F. / Vargason, J.M. / Mooers, B.H.M. / Ho, P.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions.
Authors: Eichman, B.F. / Vargason, J.M. / Mooers, B.H. / Ho, P.S.
History
DepositionNov 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0922
Polymers6,0922
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.100, 25.900, 39.900
Angle α, β, γ (deg.)90.00, 122.00, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3')


Mass: 3045.993 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMDNA11
220 mMsodium cacodylate11
350 mM11CaCl2
410 %PEG20011
530 %(v/v)PEG20012

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→33.81 Å / Num. obs: 2009 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.8
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.1 / % possible all: 91.6
Reflection
*PLUS
Num. measured all: 7532 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 91.6 %

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Processing

Software
NameVersionClassification
EPMRphasing
X-PLOR3.851refinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEAL B-DNA

Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: ANISOTROPIC B VALUES WERE APPLIED TO FCALC DURING REFINEMENT IN ORDER TO SCALE FCALC TO FOBS
RfactorNum. reflection% reflectionSelection details
Rfree0.317 178 10 %RANDOM
Rwork0.207 ---
obs0.207 1943 98.6 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.5841 Å20 Å2-1.8465 Å2
2--16.8867 Å20 Å2
3----8.3025 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 23 427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.59 Å / Total num. of bins used: 10 /
Num. reflection% reflection
Rfree22 -
Rwork144 -
obs-95.4 %

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