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- PDB-1kci: Crystal Structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridin... -

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Basic information

Entry
Database: PDB / ID: 1kci
TitleCrystal Structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide Bound to d(CGTACG)2
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / intercalator / aminoacridinecarboxamide
Function / homologyChem-DRC / DNA
Function and homology information
MethodX-RAY DIFFRACTION / ISOMORPHOUS / Resolution: 1.8 Å
AuthorsAdams, A. / Guss, J.M. / Denny, W.A. / Wakelin, L.P.G.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Crystal structure of 9-amino-N-[2-(4-morpholinyl)ethyl]-4-acridinecarboxamide bound to d(CGTACG)2: implications for structure-activity relationships of acridinecarboxamide topoisomerase poisons.
Authors: Adams, A. / Guss, J.M. / Denny, W.A. / Wakelin, L.P.
History
DepositionNov 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 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*TP*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,5103
Polymers1,8091
Non-polymers7012
Water36020
1
A: 5'-D(*CP*GP*TP*AP*CP*G)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,0206
Polymers3,6182
Non-polymers1,4024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)30.239, 30.239, 39.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-4009-

HOH

21A-4019-

HOH

31A-4020-

HOH

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DRC / 9-AMINO-N-[2-(4-MORPHOLINYL)ETHYL]-4-ACRIDINECARBOXAMIDE


Mass: 350.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6
Details: cacodylate, spermine, KCl, MgCl2, MPD, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2spermine11
3KCl11
4MgCl211
5MPD11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMsodium cacodylate1droppH6.0
20.6 mMDNA1dropduplex
31.2 mMligand1drop
46 mMspermine tetrahydrochloride1drop
540 mM1dropKCl
610 mM1dropMgCl2
75 %MPD1drop
860 %MPD1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 2000 / Details: focusing mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 1951 / Num. obs: 1951 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rsym value: 0.094 / Net I/σ(I): 21.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 5 / Num. unique all: 195 / Rsym value: 0.35 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 1955 / Num. measured all: 30670 / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.351

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: ISOMORPHOUS
Starting model: NDB entry DD0015

Resolution: 1.8→40 Å / Isotropic thermal model: isotropic / Cross valid method: Rfree / σ(F): 0 / σ(I): 0 / Stereochemistry target values: SHELX 2000 DNA dictioary
RfactorNum. reflectionSelection details
Rfree0.291 143 Random
Rwork0.215 --
all0.219 1931 -
obs0.219 1931 -
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 52 20 192
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONs_bond_d0.0040.03
X-RAY DIFFRACTIONs_angle_d0.0120.05
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_plane_restr0.0270.1
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it

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