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- PDB-1o0k: Structure of the First Parallel DNA Quadruplex-drug Complex -

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Basic information

Entry
Database: PDB / ID: 1o0k
TitleStructure of the First Parallel DNA Quadruplex-drug Complex
Components5'-D(*TP*GP*GP*GP*GP*T)-3'
KeywordsDNA / G-4 Quadruplex Drug Complex / Parallel Quadruplex
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsClark, G.R. / Pytel, P.D. / Squire, C.J. / Neidle, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Structure of the First Parallel DNA Quadruplex-drug Complex
Authors: Clark, G.R. / Pytel, P.D. / Squire, C.J. / Neidle, S.
History
DepositionFeb 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,17310
Polymers7,5214
Non-polymers1,6526
Water3,009167
1
A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules

A: 5'-D(*TP*GP*GP*GP*GP*T)-3'
B: 5'-D(*TP*GP*GP*GP*GP*T)-3'
C: 5'-D(*TP*GP*GP*GP*GP*T)-3'
D: 5'-D(*TP*GP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,34520
Polymers15,0428
Non-polymers3,30312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)53.004, 47.073, 31.865
Angle α, β, γ (deg.)90.00, 119.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1246-

HOH

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Components

#1: DNA chain
5'-D(*TP*GP*GP*GP*GP*T)-3'


Mass: 1880.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: TGGGGT synthesized by OSWEL
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DM1 / DAUNOMYCIN / DAUNORUBICIN


Mass: 527.520 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H29NO10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NaCl, Cacodylate buffer, Calcium Chloride, Spermine, MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2Cacodylate buffer11
3Calcium Chloride11
4Spermine11
5MPD11
6NaCl12
7Calcium Chloride12
8MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31
41
51
61
71
81

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Type: SSRL / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.17→99 Å / Num. obs: 20944 / % possible obs: 95.3 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.67
Reflection shellResolution: 1.17→1.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 6.8 / Num. unique all: 2031 / % possible all: 87.7
Reflection
*PLUS
Num. measured all: 202689

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The first G4 quadruplex from UDF062

Resolution: 1.17→10 Å / Isotropic thermal model: Anisotropic, isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: SHELX
Num. reflectionSelection details
all20944 -
obs18761 -
Rfree-Random
Refinement stepCycle: LAST / Resolution: 1.17→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 434 117 167 718
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.197 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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