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- PDB-1lp7: Crystal Structure of a Non-Self Complementary DNA Dodecamer Conta... -

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Basic information

Entry
Database: PDB / ID: 1lp7
TitleCrystal Structure of a Non-Self Complementary DNA Dodecamer Containing an A/T Tract: Analysis of the Effect of Crystal Environment on Local Helical Parameters
Components
  • 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*AP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*TP*TP*AP*TP*AP*TP*GP*CP*G)-3'
KeywordsDNA / A-TRACT / CRYSTAL ENVIRONMENT / LATTICE ENVIRONMENT / B-DNA / DODECAMER / CRYSTAL / DUPLEX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTodd, A.K. / Neidle, S.
CitationJournal: To be Published
Title: Crystal Structure of a Non-Self Complementary DNA Dodecamer Containing an A/T Tract: Analysis of the Effect of Crystal Environment on Local Helical Parameters
Authors: Todd, A.K. / Neidle, S.
History
DepositionMay 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3493
Polymers7,3252
Non-polymers241
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.083, 39.908, 66.469
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(*CP*GP*CP*TP*TP*AP*TP*AP*TP*GP*CP*G)-3'


Mass: 3653.390 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*CP*AP*TP*AP*TP*AP*AP*GP*CP*G)-3'


Mass: 3671.418 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, sodium cacodylate, spermine, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 249K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3spermine11
4MgCl211

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2001
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. obs: 2887 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.061
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.104 / Num. unique all: 282 / % possible all: 97.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→99 Å / σ(F): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman,Acta Cryst. D, 52, 57-64 (1996).
RfactorNum. reflectionSelection details
Rfree0.293 259 RANDOM
Rwork0.229 --
all-2799 -
obs-2799 -
Refinement stepCycle: LAST / Resolution: 2.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 485 7 88 580
LS refinement shellResolution: 2.4→2.51 Å /
RfactorNum. reflection
Rfree0.426 35
Rwork0.375 -

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