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- PDB-1m69: Atomic Resolution Structure of 5Br-9amino-DACA with d[CGTACG]2 -

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Basic information

Entry
Database: PDB / ID: 1m69
TitleAtomic Resolution Structure of 5Br-9amino-DACA with d[CGTACG]2
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / atomic resolution / adenine-thymine disorder / topoisomerase II poison
Function / homologyChem-DAX / SPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsTeixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Cardin, C.J.
Citation
Journal: To be Published
Title: Heavy Going: the Atomic Resolution Structure of a Topoisomerase II Poison Intercalating into DNA in Multiple Orientations Also Reveals a Multiple Adenine-Thymine Hydrogen Bonding Pattern
Authors: Teixeira, S.C.M. / Thorpe, J.H. / Todd, A.K. / Cardin, C.J.
#1: Journal: Thesis / Year: 1999
Title: Reading University: Single Crystal X-Ray Diffraction Studies of DNA and DNA-drug complexes
Authors: Todd, A.K.
History
DepositionJul 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2012Group: Derived calculations
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,7904
Polymers1,8091
Non-polymers9813
Water66737
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)5,5808
Polymers3,6182
Non-polymers1,9626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)30.186, 30.186, 39.443
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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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-DAX / 5-BROMO-N[2-(DIMETHYLAMINO)ETHYL]-9-AMINOACRIDINE-4-CARBOXAMIDE


Mass: 389.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21BrN4O
#3: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.31 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium acetate, magnesium acetate, sodium cacodylate, PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium acetate11
2magnesium acetate11
3sodium cacodylate11
4PEG 800011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8068 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2001
RadiationMonochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8068 Å / Relative weight: 1
ReflectionResolution: 1.1→10 Å / Num. obs: 8308 / % possible obs: 94.72 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shellResolution: 1.1→1.15 Å / % possible all: 95.79

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Processing

Software
NameClassification
MAR345data collection
XDSdata reduction
SHELXmodel building
SHELXL-97refinement
XDSdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ddf073 structure, with corrected sequence

Resolution: 1.1→10 Å / Num. parameters: 2113 / Num. restraintsaints: 3689 / Cross valid method: FREE R / σ(F): 4
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 408 5.2 %RANDOM
Rwork0.1325 ---
all0.1325 7900 --
obs0.1325 7350 94.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 81 / Occupancy sum non hydrogen: 190.25
Refinement stepCycle: LAST / Resolution: 1.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 55 37 212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.037
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0.07
X-RAY DIFFRACTIONs_from_restr_planes0.0028
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.046
X-RAY DIFFRACTIONs_approx_iso_adps0
LS refinement shellResolution: 1.1→1.15 Å /
Rfactor% reflection
Rwork0.177 -
obs-95.79 %

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