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- PDB-1ljx: THE STRUCTURE OF D(TPGPCPGPCPA)2 AT 293K: COMPARISON OF THE EFFEC... -

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Basic information

Entry
Database: PDB / ID: 1ljx
TitleTHE STRUCTURE OF D(TPGPCPGPCPA)2 AT 293K: COMPARISON OF THE EFFECT OF SEQUENCE AND TEMPERATURE
Components5'-D(*TP*GP*CP*GP*CP*A)-3'
KeywordsDNA / Z-DNA hexamer with AT base pairs at the terminal
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsThiyagarajan, S. / Satheesh Kumar, P. / Rajan, S.S. / Gautham, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature.
Authors: Thiyagarajan, S. / Satheesh Kumar, P. / Rajan, S.S. / Gautham, N.
History
DepositionApr 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: 5'-D(*TP*GP*CP*GP*CP*A)-3'
B: 5'-D(*TP*GP*CP*GP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6674
Polymers3,6182
Non-polymers492
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.182, 28.363, 44.440
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(*TP*GP*CP*GP*CP*A)-3'


Mass: 1809.218 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.84 Å3/Da / Density % sol: 33.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: cacodylate, MgCl2, cobalt hexaamine chloride, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2MgCl211
3cobalt hexaamine chloride11
4MPD11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMDNA1droppH7.0
2150 mMcobalt hexammine chloride1drop
325 mM1dropMgCl2
435 %methyl pentanediol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 15, 1998 / Details: FRANK
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→19 Å / Num. all: 3564 / Num. obs: 3468 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.045
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 19 Å / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MAR345data collection
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DCG with its terminal bases modified

1dcg


Resolution: 1.64→19 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.267 339 10 %RANDOM
Rwork0.212 ---
all-3824 --
obs-3368 --
Refinement stepCycle: LAST / Resolution: 1.64→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 2 58 300
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS

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