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- PDB-1d65: MOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN E... -

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Basic information

Entry
Database: PDB / ID: 1d65
TitleMOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN EXAMINATION OF PROPELLER TWIST AND MINOR-GROOVE WATER STRUCTURE AT 2.2 ANGSTROMS RESOLUTION
ComponentsDNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsEdwards, K.J. / Brown, D.G. / Spink, N. / Neidle, S.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.
Authors: Edwards, K.J. / Brown, D.G. / Spink, N. / Skelly, J.V. / Neidle, S.
History
DepositionMar 2, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 15, 1993Provider: 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 / 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*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.870, 40.900, 65.640
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*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')


Mass: 3662.404 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5NA CACODYLATE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlDNA1drop3mM
2100 mM1drop0.002mlMgCl2
32 mMspermine1drop0.002ml
45 mMpentamidine1drop0.006ml
530 %(v/v)MPD1drop0.005ml
630 mMsodium cacodylate1drop
740 %(v/v)1reservoir

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 9704 / Num. obs: 2943
Reflection
*PLUS
Num. all: 3402 / % possible obs: 86.5 % / Num. measured all: 12896 / Rmerge(I) obs: 0.0442
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.4 Å / Num. possible: 540 / Num. unique obs: 220

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(I): 2 /
RfactorNum. reflection
obs0.181 2502
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 71 557
Refine LS restraints
Refine-IDTypeDev ideal
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_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.016
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.033
X-RAY DIFFRACTIONn_phos_bond_d0.033
X-RAY DIFFRACTIONn_phos_bond_angle_d0.04
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONn_bond_d0.04
X-RAY DIFFRACTIONn_angle_d0.04
X-RAY DIFFRACTIONn_plane_restr0.030.025
X-RAY DIFFRACTIONn_chiral_restr0.10.067

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