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- PDB-3cco: Structural adaptation and conservation in quadruplex-drug recognition -

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Basic information

Entry
Database: PDB / ID: 3cco
TitleStructural adaptation and conservation in quadruplex-drug recognition
ComponentsDNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
KeywordsDNA / QUADRUPLEX / PROPELLER / DIMERIC / HUMAN TELOMERE PARALLEL STRANDED / LIGAND / COMPLEX / naphthalene diimidine
Function / homology: / Chem-NII / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsParkinson, G.N. / Neidle, S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Topology conservation and loop flexibility in quadruplex-drug recognition: crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes
Authors: Parkinson, G.N. / Cuenca, F. / Neidle, S.
History
DepositionFeb 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6628
Polymers3,7731
Non-polymers1,8887
Water50428
1
A: DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
hetero molecules

A: DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,32416
Polymers7,5472
Non-polymers3,77714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/31
Buried area880 Å2
ΔGint-25 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.350, 61.350, 43.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-30-

K

21A-31-

K

31A-32-

K

41A-3-

NII

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Components

#1: DNA chain DNA (5'-D(*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3') / TELOMERE REPEAT SEQUENCE


Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN HUMANS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NII / 2,7-bis[3-(dimethylamino)propyl]-4,9-bis[(3-hydroxypropyl)amino]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone


Mass: 582.691 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C30H42N6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300mM sodium chloride, 50mM sodium cacodylate pH 6.5, 30% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium chloride11
2sodium cacodylate11
3MPD11
4HOH11
5sodium chloride12
6sodium cacodylate12
7MPD12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 7, 2007 / Details: MONOCHROMATOR
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.97→22.69 Å / Num. all: 3739 / Num. obs: 3697 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.3
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.134 / Mean I/σ(I) obs: 10.8 / Num. unique all: 359 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KF1

1kf1


Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.894 / SU B: 6.344 / SU ML: 0.167 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.348 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30275 123 4.7 %RANDOM
Rwork0.25436 ---
all0.25664 2520 --
obs0.25664 2520 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.7 Å20 Å2
2--1.39 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 219 130 28 377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021381
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3063574
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.247
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.02190
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3940.2108
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3530.2228
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3180.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2320.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3970.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1010.23
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.923689
X-RAY DIFFRACTIONr_scangle_it3.3894.5574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.567 5 -
Rwork0.324 178 -
obs-178 100 %

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