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- PDB-1fn1: CRYSTAL STRUCTURE OF 9-AMINO-(N-(2-DIMETHYLAMINO)BUTYL)ACRIDINE-4... -

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Basic information

Entry
Database: PDB / ID: 1fn1
TitleCRYSTAL STRUCTURE OF 9-AMINO-(N-(2-DIMETHYLAMINO)BUTYL)ACRIDINE-4-CARBOXAMIDE BOUND TO D(CG(5BR)UACG)2
Components
  • DNA (5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3')
  • DNA (5'-D(P*GP*(BRO)UP*AP*CP*G)-3')
KeywordsDNA / 9-aminoacridine-4-carboamide / hexanucleotide / intercalation / quadruplex
Function / homologyChem-8AD / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsAdams, A. / Guss, J.M. / Collyer, C.A. / Denny, W.A. / Wakelin, L.P.G.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: A novel form of intercalation involving four DNA duplexes in an acridine-4-carboxamide complex of d(CGTACG)(2).
Authors: Adams, A. / Guss, J.M. / Collyer, C.A. / Denny, W.A. / Wakelin, L.P.
History
DepositionAug 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.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: DNA (5'-D(P*GP*(BRO)UP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9135
Polymers3,4592
Non-polymers4543
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.880, 53.168, 40.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Cell settingorthorhombic
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-3014-

8AD

21B-4001-

CO

31A-4016-

HOH

41A-4018-

HOH

51B-4003-

HOH

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Components

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


Mass: 1584.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KNOWN TO BE A GOOD SEQUENCE FOR INTERCALATION
#2: DNA chain DNA (5'-D(*CP*GP*(BRO)UP*AP*CP*G)-3')


Mass: 1874.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KNOWN TO BE A GOOD SEQUENCE FOR INTERCALATION
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-8AD / 9-AMINO-(N-(2-DIMETHYLAMINO)BUTYL)ACRIDINE-4-CARBOXAMIDE


Mass: 336.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N4O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 6.5
Details: MPD, sodium cacodylate, magnesium acetate, cobalt(II) chloride, spermine, pH 6.5, VAPOR DIFFUSION, temperature 285K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2magnesium acetate11
3CoCl211
4spermine11
5MPD11
6MPD12
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mM1drop
20.5 mMDNA1dropdouble-stranded conc.
33 mMmagnesium acetate1drop
40.5 mM1dropCoCl2
54.5 mMspermine1drop
61 mM9-aminobutyl-DACA1drop
77 %MPD1drop
835 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.892
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 29, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.892 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 4345 / Num. obs: 4345 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 37
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 9.1 / Num. unique all: 739 / % possible all: 95
Reflection
*PLUS

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Processing

Software
NameClassification
SHELXL-97refinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→40 Å / Num. parameters: 1123 / Num. restraintsaints: 2727 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Shelx 2000
RfactorNum. reflection% reflectionSelection details
Rfree0.24 608 7.8 %Random
Rwork0.23 ---
all0.23 7785 --
obs0.23 7785 100 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 251.75
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 222 34 19 275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_similar_dist0.038
X-RAY DIFFRACTIONs_from_restr_planes0.0145
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.01
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.8 % / Rfactor all: 0.23 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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