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- PDB-1d48: STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA (MAGNESIUM FREE) AT ... -

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Basic information

Entry
Database: PDB / ID: 1d48
TitleSTRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA (MAGNESIUM FREE) AT 1 ANGSTROM RESOLUTION
ComponentsDNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
KeywordsDNA / Z-DNA / DOUBLE HELIX
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1 Å
AuthorsEgli, M. / Williams, L.D. / Gao, Q. / Rich, A.
CitationJournal: Biochemistry / Year: 1991
Title: Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution.
Authors: Egli, M. / Williams, L.D. / Gao, Q. / Rich, A.
History
DepositionSep 11, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.405, 30.768, 43.152
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*GP*CP*G)-3')


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.69 Å3/Da / Density % sol: 27.11 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2SPERMINE11
3WATER12
4MPD12
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 mMDNA1drop
220 mMsodium cacodylate1drop
315 mMspermine tetrachloride1drop
420 %1reservoir

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1 Å / Num. all: 10900 / Num. obs: 8200 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1 Å / Lowest resolution: 1.2 Å / % possible obs: 35 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.002

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Processing

Software
NameVersionClassification
PROLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementHighest resolution: 1 Å / σ(F): 2 /
RfactorNum. reflection
obs0.185 8183
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 47 301
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.185 / Num. reflection obs: 8183
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 5 Å / Lowest resolution: 10 Å / Total num. of bins used: 8 / Rfactor all: 0.185

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