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- PDB-167d: THE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BE... -

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Basic information

Entry
Database: PDB / ID: 167d
TitleTHE CRYSTAL STRUCTURE OF C-C-A-T-T-A-A-T-G-G: IMPLICATIONS FOR BENDING OF B-DNA AT T-A STEPS
ComponentsDNA (5'-D(*CP*CP*AP*TP*TP*AP*AP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsGoodsell, D.S. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps.
Authors: Goodsell, D.S. / Kaczor-Grzeskowiak, M. / Dickerson, R.E.
History
DepositionApr 4, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0882
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.200, 33.200, 96.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-27-

HOH

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Components

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


Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4WATER12
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion standing drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.39 mMDNA1drop
2140 mM1dropMgCl2
315 %(v/v)MPD1drop
435 %MPD1reservoir
51

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Data collection

DiffractionMean temperature: 277 K
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 2726 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 2.3 Å / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.0238

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.3→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.2 2726
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 44 448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it6.6126
X-RAY DIFFRACTIONn_sugar_angle_it8.0696
X-RAY DIFFRACTIONn_phos_bond_it6.326
X-RAY DIFFRACTIONn_phos_angle_it7.9436
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0310.03
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0580.04
X-RAY DIFFRACTIONn_phos_bond_d0.0350.025
X-RAY DIFFRACTIONn_phos_bond_angle_d0.090.05
X-RAY DIFFRACTIONn_plane_restr0.020.02
X-RAY DIFFRACTIONn_chiral_restr0.1770.15
X-RAY DIFFRACTIONn_singtor_nbd0.1040.1
X-RAY DIFFRACTIONn_multtor_nbd0.10.1
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d

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