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- PDB-1zje: 12mer-spd -

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Basic information

Entry
Database: PDB / ID: 1zje
Title12mer-spd
Components
  • 5'-D(*AP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*T)-3'
  • 5'-D(*TP*AP*GP*CP*CP*CP*CP*GP*CP*CP*CP*C)-3'
KeywordsDNA / flipped-out base / A-DNA
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDohm, J.A. / Hsu, M.H. / Hwu, J.R. / Huang, R.C. / Moudrianakis, E.N. / Lattman, E.E. / Gittis, A.G.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Influence of Ions, Hydration, and the Transcriptional Inhibitor P4N on the Conformations of the Sp1 Binding Site.
Authors: Dohm, J.A. / Hsu, M.H. / Hwu, J.R. / Huang, R.C. / Moudrianakis, E.N. / Lattman, E.E. / Gittis, A.G.
History
DepositionApr 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: 5'-D(*AP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*T)-3'
B: 5'-D(*TP*AP*GP*CP*CP*CP*CP*GP*CP*CP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3292
Polymers7,3292
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.541, 39.687, 42.166
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 5'-D(*AP*GP*GP*GP*GP*CP*GP*GP*GP*GP*CP*T)-3'


Mass: 3784.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Ordered from Biosource
#2: DNA chain 5'-D(*TP*AP*GP*CP*CP*CP*CP*GP*CP*CP*CP*C)-3'


Mass: 3544.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Ordered from Biosource
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, bis tris propane, spermidine, sodium chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 4103 / Num. obs: 3935 / % possible obs: 95.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2→2.07 Å / % possible all: 88.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→15 Å / σ(F): 0 / Stereochemistry target values: CNS nucleic acid files
Details: 12mer-spd was grown in the presence of spermidine, but no spermidine molecules were visualized in the maps.
RfactorNum. reflectionSelection details
Rfree0.2561 278 RANDOM
Rwork0.2168 --
all0.2167 3527 -
obs0.2117 3394 -
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 30 516

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