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- PDB-3qsc: The first crystal structure of a human telomeric G-quadruplex DNA... -

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Basic information

Entry
Database: PDB / ID: 3qsc
TitleThe first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a copper complex)
Components5'-D(*AP*GP*GP*GP*TP*(BRU)P*AP*GP*GP*GP*TP*T)-3'
KeywordsDNA / Parallel / telomere / quadruplex / drug / metal complex / copper complex
Function / homologyChem-CUF / : / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCampbell, N.H. / Abd Karim, N.H. / Parkinson, G.N. / Vilar, R. / Neidle, S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes.
Authors: Campbell, N.H. / Karim, N.H. / Parkinson, G.N. / Gunaratnam, M. / Petrucci, V. / Todd, A.K. / Vilar, R. / Neidle, S.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Sep 13, 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 / 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_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
X: 5'-D(*AP*GP*GP*GP*TP*(BRU)P*AP*GP*GP*GP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,6245
Polymers3,8381
Non-polymers7864
Water48627
1
X: 5'-D(*AP*GP*GP*GP*TP*(BRU)P*AP*GP*GP*GP*TP*T)-3'
hetero molecules

X: 5'-D(*AP*GP*GP*GP*TP*(BRU)P*AP*GP*GP*GP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,24810
Polymers7,6772
Non-polymers1,5718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2240 Å2
ΔGint3 kcal/mol
Surface area4850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.753, 54.786, 33.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11X-2013-

K

21X-2014-

K

31X-2015-

K

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Components

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


Mass: 3838.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CUF / [2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappaO}(2-)]copper (II) / N,N-Bis[4-[[1-(2-ethyl)piperidine]oxy]salicylidene]-4,5-difluoro-1,2-phenylenediamine-Copper (II)


Mass: 668.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38CuF2N4O4
#4: 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Initial conditions were 0.6 mM quadruplex DNA, 0.6 mM ligand, 0.4% PEG 2000 (w/v), 100mM potassium chloride, 100mM sodium chloride, 100mM lithium sulphate, 20mM potassium cacodylate, ...Details: Initial conditions were 0.6 mM quadruplex DNA, 0.6 mM ligand, 0.4% PEG 2000 (w/v), 100mM potassium chloride, 100mM sodium chloride, 100mM lithium sulphate, 20mM potassium cacodylate, equilibrated against a reservoir well solution of 60% PEG 2000 (w/v), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.90740, 0.92060, 0.92110
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.90741
20.92061
30.92111
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 3.4 / Number: 6416 / Rsym value: 0.101 / D res high: 2.352 Å / D res low: 23.805 Å / Num. obs: 1774 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.4423.8196.610.030.033.1
5.267.4498.410.0510.0513.1
4.295.2698.110.0610.0613.5
3.724.2998.610.0740.0743.6
3.333.7299.110.1070.1073.7
3.043.3399.410.1770.1773.7
2.813.0410010.2140.2143.8
2.632.8199.810.2730.2733.8
2.482.6399.810.3560.3563.8
2.352.4899.810.4180.4183.6
ReflectionResolution: 2.254→21.188 Å / Num. all: 2020 / Num. obs: 2020 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.034 / Net I/σ(I): 24.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.382.60.0958.17012710.09591.5
2.38-2.524.20.06211.811742820.06299.9
2.52-2.694.30.0441510802540.044100
2.69-2.914.20.03916.210162430.039100
2.91-3.194.10.03116.29402270.031100
3.19-3.564.10.03214.38061990.03298.8
3.56-4.1240.02819.87371850.02899.8
4.12-5.043.70.03615.86071620.03699.6
5.04-7.133.40.0317.34281270.0398.8
7.13-21.8763.10.03118.5220700.03190.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
SHELXDphasing
RefinementMethod to determine structure: MAD
Starting model: 1K8P

1k8p


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2684 / WRfactor Rwork: 0.2426 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.7823 / SU B: 8.628 / SU ML: 0.181 / SU R Cruickshank DPI: 0.4643 / SU Rfree: 0.2498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 77 4.6 %RANDOM
Rwork0.2132 ---
obs0.2142 1687 99.06 %-
all-1687 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.48 Å2 / Biso mean: 35.2997 Å2 / Biso min: 13.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.84 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 231 48 27 306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021312
X-RAY DIFFRACTIONr_angle_refined_deg1.5593476
X-RAY DIFFRACTIONr_chiral_restr0.0560.244
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02169
X-RAY DIFFRACTIONr_scbond_it2.8473312
X-RAY DIFFRACTIONr_scangle_it4.314.5476
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 6 -
Rwork0.337 107 -
all-113 -
obs-107 100 %

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