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- PDB-3q5c: Crystal structure of four-way junction with sticky end -

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Basic information

Entry
Database: PDB / ID: 3q5c
TitleCrystal structure of four-way junction with sticky end
ComponentsDNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')
KeywordsDNA / Sticky end
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')
B: DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')
C: DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')
D: DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,1884
Polymers12,1884
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-10 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.640, 33.841, 40.400
Angle α, β, γ (deg.)112.77, 90.00, 110.44
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain
DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3')


Mass: 3046.980 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1mM DNA, 50mM Cacodylate buffer, 50mM CaCl2, 1mM spermine, 50% MPD in Reservior, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9922 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9922 Å / Relative weight: 1
ReflectionResolution: 2.5→36.8 Å / Num. all: 3708 / Num. obs: 3490 / % possible obs: 94.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.13 / Net I/σ(I): 3.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 1.4 / Num. unique all: 535 / Rsym value: 0.393 / % possible all: 93.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P4Y

1p4y


Resolution: 2.501→29.357 Å / SU ML: 0 / Cross valid method: Throught / σ(F): 0.01 / Phase error: 41.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 145 4.33 %RANDOM
Rwork0.2407 ---
obs0.2425 3449 90.42 %-
all-3606 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.602 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 51.6479 Å2
Baniso -1Baniso -2Baniso -3
1-27.9058 Å25.2849 Å2-8.3794 Å2
2---27.2791 Å24.1963 Å2
3----0.6267 Å2
Refinement stepCycle: LAST / Resolution: 2.501→29.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 0 9 817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016904
X-RAY DIFFRACTIONf_angle_d2.7391388
X-RAY DIFFRACTIONf_chiral_restr0.11156
X-RAY DIFFRACTIONf_plane_restr0.00840
X-RAY DIFFRACTIONf_dihedral_angle_d36.143384

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