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- PDB-1xcu: oligonucleotid/drug complex -

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Basic information

Entry
Database: PDB / ID: 1xcu
Titleoligonucleotid/drug complex
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / ANTHRAQUINONE / CO2+
Function / homologyChem-AN9 / : / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsValls, N. / Steiner, R.A. / Wright, G. / Murshudov, G.N. / Subirana, J.A.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2005
Title: Variable role of ions in two drug intercalation complexes of DNA
Authors: Valls, N. / Steiner, R.A. / Wright, G. / Murshudov, G.N. / Subirana, J.A.
History
DepositionSep 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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 / pdbx_struct_special_symmetry / 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.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

Downloads & links

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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)4,9419
Polymers3,6182
Non-polymers1,3227
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.056, 52.856, 40.084
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-41-

AN9

21B-32-

CO

31B-34-

BA

41B-36-

NA

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Components

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DNA chain , 1 types, 2 molecules AB

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 5 types, 34 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AN9 / 1,5-BIS[3-(DIETHYLAMINO)PROPIONAMIDO]ANTHRACENE-9,10-DIONE


Mass: 492.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H36N4O4
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: drug, barium chloride, cobalt chloride, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1drug11
2barium chloride11
3cobalt choloride11
4MPD11
5drug12
6barium chloride12
7cobalt choloride12
8MPD12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.79986 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79986 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 2190 / Redundancy: 16.4 % / Rmerge(I) obs: 0.035
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.247 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25162 205 9.4 %RANDOM
Rwork0.21299 ---
all0.2168 ---
obs0.21683 1984 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.494 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2---2.25 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 225 47 28 300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021307
X-RAY DIFFRACTIONr_angle_refined_deg2.1273453
X-RAY DIFFRACTIONr_chiral_restr0.0820.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02161
X-RAY DIFFRACTIONr_nbd_refined0.20.274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.219
X-RAY DIFFRACTIONr_metal_ion_refined0.1280.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.218
X-RAY DIFFRACTIONr_mcbond_it1.9391.55
X-RAY DIFFRACTIONr_scbond_it2.283298
X-RAY DIFFRACTIONr_scangle_it2.9694.5453
LS refinement shellResolution: 1.997→2.048 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.259 9
Rwork0.193 116

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