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- PDB-3qk4: Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 3qk4
TitleCrystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex
ComponentsDNA (5'-D(*CP*GP*CP*GP*GP*GP*TP*AP*CP*CP*CP*GP*CP*G)-3')
KeywordsDNA / A-DNA duplex
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2)
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionJan 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,5662
Polymers8,5662
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-1 kcal/mol
Surface area5230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.988, 28.988, 87.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 4282.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.99
Details: The drop consist of 1mM DNA, 50mM buffer, 10mM BaCl2, 1mM Spermine equilibriated against 50% MPD, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 17, 2008 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.673
11-H, K, -L20.327
ReflectionResolution: 2.6→20 Å / Num. all: 2256 / Num. obs: 2171 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.67 % / Biso Wilson estimate: 57.76 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.0714 / Net I/σ(I): 4.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.4184 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.3936 / % possible all: 95.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0109refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-DNA fiber Model

Resolution: 2.6→19.96 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.866 / SU B: 14.13 / SU ML: 0.297 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 126 5.8 %RANDOM
Rwork0.2458 ---
obs0.24734 2042 97.18 %-
all-2168 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.531 Å2
Baniso -1Baniso -2Baniso -3
1-18.22 Å20 Å20 Å2
2--18.22 Å20 Å2
3----36.44 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 568 0 46 614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.9753978
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1520.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 3 -
Rwork0.443 141 -
obs--94.74 %

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