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- PDB-1z3f: Structure of ellipticine in complex with a 6-bp DNA -

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Basic information

Entry
Database: PDB / ID: 1z3f
TitleStructure of ellipticine in complex with a 6-bp DNA
Components5'-D(*CP*GP*AP*TP*CP*G)-3'
KeywordsDNA / ANTICANCER / DNA BINDING / DRUG DESIGN / ELLIPTICINE / INTERCALATOR
Function / homology: / ELLIPTICINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCanals, A. / Purciolas, M. / Aymami, J. / Coll, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The anticancer agent ellipticine unwinds DNA by intercalative binding in an orientation parallel to base pairs.
Authors: Canals, A. / Purciolas, M. / Aymami, J. / Coll, M.
History
DepositionMar 12, 2005Deposition 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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*AP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2907
Polymers3,6182
Non-polymers6715
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.860, 24.860, 78.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-EL / ELLIPTICINE / Ellipticine


Mass: 247.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N2 / Comment: alkaloid*YM
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water / 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: 1.62 Å3/Da / Density % sol: 23.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, sodium cacodylate, cobalt hexammine, sodium chloride, potassium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3cobalt hexamine11
4sodium chloride11
5potassium chloride11
6H2O11
7MPD12
8sodium cacodylate12
9cobalt hexamine12
10potassium chloride12
11H2O12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 14, 2004 / Details: microfocus beamline
RadiationMonochromator: liq. N2 cooled Si-111 double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→16.66 Å / Num. all: 4436 / Num. obs: 4420 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.5→1.54 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→16.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.971 / SU B: 6.257 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24166 221 5 %RANDOM
Rwork0.22041 ---
all0.22 ---
obs0.2217 4197 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.952 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.6 Å20 Å2
2--1.19 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 1.5→16.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 41 27 308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021312
X-RAY DIFFRACTIONr_angle_refined_deg2.5053476
X-RAY DIFFRACTIONr_chiral_restr0.0920.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02162
X-RAY DIFFRACTIONr_nbd_refined0.1690.2107
X-RAY DIFFRACTIONr_nbtor_refined0.3350.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0260.21
X-RAY DIFFRACTIONr_scbond_it4.0893590
X-RAY DIFFRACTIONr_scangle_it3.0534.5476
X-RAY DIFFRACTIONr_rigid_bond_restr8.4653590
X-RAY DIFFRACTIONr_sphericity_free6.374330
X-RAY DIFFRACTIONr_sphericity_bonded4.1973278
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 16 -
Rwork0.24 317 -
obs--100 %

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