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- PDB-1d76: CRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT CONTAINING A 2-... -

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Basic information

Entry
Database: PDB / ID: 1d76
TitleCRYSTAL AND MOLECULAR STRUCTURE OF A DNA FRAGMENT CONTAINING A 2-AMINO ADENINE MODIFICATION: THE RELATIONSHIP BETWEEN CONFORMATION, PACKING, AND HYDRATION IN Z-DNA HEXAMERS
ComponentsDNA (5'-D(*CP*GP*UP*(1AP)P*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX / MODIFIED
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.3 Å
AuthorsSchneider, B. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M.
CitationJournal: Biochemistry / Year: 1992
Title: Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers.
Authors: Schneider, B. / Ginell, S.L. / Jones, R. / Gaffney, B. / Berman, H.M.
History
DepositionMay 19, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Sep 15, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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*UP*(1AP)P*CP*G)-3')
B: DNA (5'-D(*CP*GP*UP*(1AP)P*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)3,6202
Polymers3,6202
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)17.944, 31.282, 44.701
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*UP*(1AP)P*CP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.73 Å3/Da / Density % sol: 27.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: sitting drop / Details: hanging drop also O. K.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.9 mMDNA1drop
230 mMsodium cacodylate1drop
315 mM1dropMgCl2
45 mMspermine tetrachloride1drop
520 %MPD1drop
648 %MPD1reservoir
71

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.02→45 Å / Num. all: 13324 / Num. obs: 5790 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 1.02 Å / Observed criterion σ(I): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.3→8 Å / σ(F): 4 /
RfactorNum. reflection
obs0.138 4588
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
WATERS 1 TO 70X-RAY DIFFRACTIONTRisotropic
WATERS 71 TO 84X-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 238 2 84 324
Refinement
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 8 Å / σ(F): 4 / Rfactor obs: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS

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