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- PDB-1d77: CRYSTAL STRUCTURE OF A B-DNA DODECAMER CONTAINING INOSINE, D(CGCI... -

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Basic information

Entry
Database: PDB / ID: 1d77
TitleCRYSTAL STRUCTURE OF A B-DNA DODECAMER CONTAINING INOSINE, D(CGCIAATTCGCG), AT 2.4 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER B-DNA DODECAMERS
ComponentsDNA (5'-D(*CP*GP*CP*IP*AP*AP*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsXuan, J.C. / Weber, I.T.
CitationJournal: Nucleic Acids Res. / Year: 1992
Title: Crystal structure of a B-DNA dodecamer containing inosine, d(CGCIAATTCGCG), at 2.4 A resolution and its comparison with other B-DNA dodecamers.
Authors: Xuan, J.C. / Weber, I.T.
History
DepositionMay 30, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2012Group: Other
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,2972
Polymers7,2972
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)24.900, 40.400, 66.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3648.378 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MG ACETATE11
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.25 mg/mlDNA1drop
28 mMmagnesium acetate1drop
30.7 mMspermine1drop
412.5 %MPD1drop
525 %MPD1reservoir
61

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 2492
Reflection
*PLUS
Highest resolution: 2.4 Å / Rmerge F obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 46.3 %

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.4→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.174 2256
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 484 0 44 528
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_it4.6317.5
X-RAY DIFFRACTIONn_sugar_angle_it5.3927.5
X-RAY DIFFRACTIONn_phos_bond_it5.8147.5
X-RAY DIFFRACTIONn_phos_angle_it9.4117.5
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.0120.025
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0430.05
X-RAY DIFFRACTIONn_phos_bond_d0.0460.05
X-RAY DIFFRACTIONn_phos_bond_angle_d0.1010.075
X-RAY DIFFRACTIONn_plane_restr0.0180.03
X-RAY DIFFRACTIONn_chiral_restr0.0770.1
X-RAY DIFFRACTIONn_singtor_nbd0.1610.063
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Num. reflection obs: 2256 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.7 Å2

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