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- PDB-1xcs: structure of oligonucleotide/drug complex -

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Basic information

Entry
Database: PDB / ID: 1xcs
Titlestructure of oligonucleotide/drug complex
Components5'-D(*CP*GP*TP*AP*CP*G)-3'
KeywordsDNA / DRUG-DNA COMPLEX / DOUBLE HELIX / CO2+
Function / homologyChem-A4L / : / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.3Nov 16, 2011Group: Atomic model
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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr1_symmetry / _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)4,8016
Polymers3,6182
Non-polymers1,1834
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.659, 53.473, 40.691
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
11B-63-

CO

21B-65-

BA

31B-85-

HOH

41B-86-

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.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-A4L / 9-[(5-(ACETYLAMINO)-6-{[(1S,4R)-8-AMINO-4-[((2R)-6-AMINO-2-{2-[(1S)-5-AMINO-1-FORMYLPENTYL]HYDRAZINO}HEXANOYL)AMINO]-1-(4-AMINOBUTYL)-2,3-DIOXOOCTYL]AMINO}-6-OXOHEXYL)AMINO]-6-CHLORO-2-METHOXYACRIDINIUM


Mass: 927.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H73ClN11O7
#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, barium chloride, cobalt chloride, drug, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2barium chloride11
3cobalt chloride11
4drug11
5MPD12
6barium chloride12
7cobalt chloride12
8drug12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.4→40.82 Å / Num. obs: 6152 / Rsym value: 0.082
Reflection shellResolution: 1.4→1.45 Å / Rsym value: 0.117

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.112 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25091 602 9.8 %RANDOM
Rwork0.19348 ---
all0.202 ---
obs0.19882 5550 96.09 %-
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: 21.894 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 225 31 44 300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021281
X-RAY DIFFRACTIONr_bond_other_d0.0040.02131
X-RAY DIFFRACTIONr_angle_refined_deg2.1473426
X-RAY DIFFRACTIONr_angle_other_deg1.6113322
X-RAY DIFFRACTIONr_chiral_restr0.0930.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02144
X-RAY DIFFRACTIONr_gen_planes_other0.0120.0212
X-RAY DIFFRACTIONr_nbd_refined0.1980.282
X-RAY DIFFRACTIONr_nbd_other0.2570.2185
X-RAY DIFFRACTIONr_nbtor_other0.1290.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.230
X-RAY DIFFRACTIONr_metal_ion_refined0.2150.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6790.29
X-RAY DIFFRACTIONr_scbond_it1.9943281
X-RAY DIFFRACTIONr_scangle_it2.8754.5426
X-RAY DIFFRACTIONr_rigid_bond_restr1.2212281
X-RAY DIFFRACTIONr_sphericity_free3.403247
X-RAY DIFFRACTIONr_sphericity_bonded3.1272253
LS refinement shellResolution: 1.403→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 48
Rwork0.168 395

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