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- PDB-1p20: Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes -

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Basic information

Entry
Database: PDB / ID: 1p20
TitleSurprising Roles of Electrostatic Interactions in DNA-Ligand Complexes
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / adriamycin / intercalation / electrostatics / thallium
Function / homologyDOXORUBICIN / THALLIUM (I) ION / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsHowerton, S.B. / Nagpal, A. / Williams, L.D.
CitationJournal: Biopolymers / Year: 2003
Title: Surprising Roles of Electrostatic Interactions in DNA-Ligand Complexes
Authors: Howerton, S.B. / Nagpal, A. / Williams, L.D.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_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.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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,9665
Polymers1,8091
Non-polymers1,1574
Water1,04558
1
A: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,93210
Polymers3,6182
Non-polymers2,3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)27.894, 27.894, 52.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: -Y,-X,1/2-Z

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11
#3: Chemical ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tl
#4: 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: d(CGATCG), Tl acetate, Mg acetate, MPD, spermine acetate, adriamycin, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tl acetate11
2Mg acetate11
3spermine acetate11
4MPD11
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.3 mMammonium salt1drop
227.5 mMthallium acetate1droppH6.4
32.2 mMmagnesium acetate1drop
44.5 %1drop
51.3 mMspermine acetate1drop
62.5 mMchloride salt of adriamycin1drop
735 %MPD1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 3, 2001 / Details: Osmic blue multilayer confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.26→100 Å
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 5559 / % possible obs: 99.9 % / Num. measured all: 31250
Reflection shell
*PLUS
Highest resolution: 1.34 Å / % possible obs: 99.9 %

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Processing

Software
NameClassification
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NDB Entry DDF044

Resolution: 1.34→35 Å / Isotropic thermal model: isotropic
Cross valid method: throughout refinement except final round
σ(F): 2 / Stereochemistry target values: Parkinson & Berman, 1996
RfactorNum. reflection% reflectionSelection details
Rfree0.215 457 10.6 %random
Rwork0.193 ---
all0.189 5559 --
obs0.189 4302 85.5 %-
Displacement parametersBiso mean: 13.8 Å2
Refinement stepCycle: LAST / Resolution: 1.34→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 42 58 220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.67
X-RAY DIFFRACTIONc_bond_d0.02
Refinement
*PLUS
Lowest resolution: 35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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