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- PDB-3ixn: Crystal structure of d(CCGGTACCGG) as B-DNA duplex -

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Basic information

Entry
Database: PDB / ID: 3ixn
TitleCrystal structure of d(CCGGTACCGG) as B-DNA duplex
ComponentsDNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
KeywordsDNA / B-DNA
Function / homology: / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsVenkadesh, S. / Mandal, P.K. / Gautham, N.
CitationJournal: To be Published
Title: Crystal Structure of inverted repeat sequence d(CCGGTACCGG)as B-DNA duplex
Authors: Venkadesh, S. / Mandal, P.K. / Gautham, N.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2695
Polymers6,0922
Non-polymers1773
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-3 kcal/mol
Surface area3830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.940, 32.940, 94.854
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(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3')


Mass: 3045.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthethised
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5mM CoCl2, 1mM spermine, 50% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.54 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2009 / Details: Double Crystal
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.539
11-H-K, K, -L20.461
ReflectionResolution: 2.87→30 Å / Num. all: 1378 / Num. obs: 1365 / % possible obs: 99.4 % / Redundancy: 10.1 % / Biso Wilson estimate: 69.9 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.081 / Net I/σ(I): 6.2
Reflection shellResolution: 2.87→2.97 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 1.2 / Num. unique all: 135 / Rsym value: 0.279 / % possible all: 97.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fiber model built in INSIGHTII software

Resolution: 2.87→28.53 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.91 / SU B: 17.29 / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27469 63 5.2 %RANDOM
Rwork0.26146 ---
obs0.26212 1160 91.2 %-
all-1365 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.728 Å2
Baniso -1Baniso -2Baniso -3
1--16.39 Å20 Å20 Å2
2---16.39 Å20 Å2
3---32.77 Å2
Refine analyzeLuzzati coordinate error obs: 0.635 Å
Refinement stepCycle: LAST / Resolution: 2.87→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 3 11 418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.021452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.9643694
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_restr0.2270.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02210
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_it5.5683452
X-RAY DIFFRACTIONr_scangle_it7.4054.5694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.873→2.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.933 6 -
Rwork0.682 88 -
obs-91 100 %

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