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- PDB-1k2l: STRUCTURAL CHARACTERIZATION OF BISINTERCALATION IN HIGHER-ORDER D... -

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Basic information

Entry
Database: PDB / ID: 1k2l
TitleSTRUCTURAL CHARACTERIZATION OF BISINTERCALATION IN HIGHER-ORDER DNA AT A JUNCTION-LIKE QUADRUPLEX
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DNA Strand Exchange / quadruplex / bisintercalation
Function / homologyChem-BDC / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTeixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Powell, H.R. / Adams, A. / Wakelin, L.P.G. / Denny, W.A. / Cardin, C.J.
CitationJournal: J.MOL.BIOL. / Year: 2002
Title: Structural Characterisation of Bisintercalation in Higher-order DNA at a Junction-like Quadruplex
Authors: Teixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Powell, H.R. / Adams, A. / Wakelin, L.P.G. / Denny, W.A. / Cardin, C.J.
History
DepositionSep 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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(*CP*GP*TP*AP*CP*G)-3'
B: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4635
Polymers3,6182
Non-polymers8453
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.507, 53.738, 40.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-10-

CO

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Components

#1: DNA chain 5'-D(*CP*GP*TP*AP*CP*G)-3'


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-BDC / BIS-(9-OCTYLAMINO(2-DIMETHYLAMINOETHYL)ACRIDINE-4-CARBOXAMIDE / BIS-DACA


Mass: 726.952 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H54N8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.28 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium cacodylate buffer, magnesium acetate, cobalt chloride, spermine, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium cacodylate buffer11
2magnesium acetate11
3COCl211
4spermine11
5MPD11
6magnesium acetate12
7COCl212
8MPD12
Crystal grow
*PLUS
Temperature: 285 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMsodium cacodylate1droppH6.5
20.5 mMDNA duplex1drop
30.25 mMbis-DACA1drop
41 mMmagnesium acetate1drop
52 mM1dropCoCl2
66 mMspermine1drop
72 %(v/v)MPD1drop
810 %1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.28→13.5 Å / Num. all: 2063 / Num. obs: 2063 / % possible obs: 88.06 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.57
Reflection shellResolution: 2.28→2.36 Å / % possible all: 93.8
Reflection
*PLUS
Highest resolution: 2.35 Å / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→9 Å / Num. parameters: 848 / Num. restraintsaints: 1140 / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3091 92 4.7 %RANDOM
Rwork0.239 ---
all0.3268 1971 --
obs0.2452 1217 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 264
Refinement stepCycle: LAST / Resolution: 2.4→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 224 36 9 269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.016
X-RAY DIFFRACTIONs_from_restr_planes0.0001
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.053
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.009
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 2.4→2.48 Å /
Rfactor% reflection
Rwork0.322 -
obs-95.38 %
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.3094 / Rfactor Rwork: 0.2385
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d

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