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- PDB-1d28: CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG) -

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Basic information

Entry
Database: PDB / ID: 1d28
TitleCRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT: D(CGTGAATTCACG)
ComponentsDNA (5'-D(*CP*GP*TP*GP*AP*AP*TP*TP*CP*AP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsNarayana, N. / Ginell, S.L. / Russu, I.M. / Berman, H.M.
CitationJournal: Biochemistry / Year: 1991
Title: Crystal and molecular structure of a DNA fragment: d(CGTGAATTCACG).
Authors: Narayana, N. / Ginell, S.L. / Russu, I.M. / Berman, H.M.
History
DepositionDec 18, 1990Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 7, 1992Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3252
Polymers7,3252
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.780, 40.850, 65.670
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*TP*GP*AP*AP*TP*TP*CP*AP*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.: 85 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.22 mMDNA dodecamer1drop
230 mMsodium cacodylate1drop
315 mMmagnesium chloride1drop
42.0 mMspermine1drop
510 %(v/v)MPD1drop
622 %MPD1reservoir
71

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Data collection

DiffractionMean temperature: 183 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SIEMENS-NICOLET / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 2075 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 56 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0875

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.7→10 Å / σ(I): 2 /
RfactorNum. reflection
obs0.17 1532
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 85 571
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_d0.013
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.029
X-RAY DIFFRACTIONn_phos_bond_d0.031
X-RAY DIFFRACTIONn_phos_bond_angle_d0.038
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: 2.7 Å / Lowest resolution: 10 Å / σ(I): 2 / Rfactor obs: 0.17 / Num. reflection obs: 1532
Solvent computation
*PLUS
Displacement parameters
*PLUS

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