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

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Basic information

Entry
Database: PDB / ID: 3qsf
TitleThe first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a nickel complex)
Components5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*T)-3'
KeywordsDNA / Parallel / telomere / nickel / drug / metal complex
Function / homology: / Chem-NUF / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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*TP*AP*GP*GP*GP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5545
Polymers3,7731
Non-polymers7814
Water36020
1
X: 5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*T)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)9,10810
Polymers7,5472
Non-polymers1,5618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1730 Å2
ΔGint-1 kcal/mol
Surface area4770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.020, 54.909, 33.691
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

41X-20-

HOH

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Components

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


Mass: 3773.462 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-NUF / [2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) / N,N-Bis[4-[[1-(2-ethyl)piperidine]oxy]salicylidene]-4,5-difluoro-1,2-phenylenediamine-Nickel (II)


Mass: 663.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H38F2N4NiO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Initial conditions in the 3 ul drop were: 1.25mM quadruplex DNA, 1.25mM ligand, 0.83% PEG (w/v) 10 000, 16.7mM potassium chloride, 16.7mM sodium chloride, 16.7mM lithium sulphate and 20 mM ...Details: Initial conditions in the 3 ul drop were: 1.25mM quadruplex DNA, 1.25mM ligand, 0.83% PEG (w/v) 10 000, 16.7mM potassium chloride, 16.7mM sodium chloride, 16.7mM lithium sulphate and 20 mM potassium cacodylate buffer at pH 7.0. This was equilibrated against a reservoir well solution of 50% (w/v) PEG 10000 , 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: 1.4866 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4866 Å / Relative weight: 1
ReflectionResolution: 2.308→22.01 Å / Num. all: 1888 / Num. obs: 1888 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rsym value: 0.053 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.31-2.432.70.1534.66582420.15389.8
2.43-2.583.70.116.19812630.1199.2
2.58-2.763.80.0826.79192450.082100
2.76-2.983.80.0748.78632280.074100
2.98-3.263.80.05310.78292190.05399.7
3.26-3.653.60.0527.56751850.05298.5
3.65-4.213.50.0589.86341790.058100
4.21-5.163.50.0414.95311500.0499.6
5.16-7.293.30.04512.13891180.04596.1
7.29-22.013.10.04314.8183590.04380.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.36 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.01 Å
Translation2.5 Å22.01 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QSC

3qsc


Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.872 / WRfactor Rfree: 0.3649 / WRfactor Rwork: 0.2714 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.724 / SU B: 9.949 / SU ML: 0.211 / SU R Cruickshank DPI: 0.4976 / SU Rfree: 0.3403 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3203 77 4.6 %RANDOM
Rwork0.2369 ---
obs0.2404 1684 97 %-
all-1684 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.95 Å2 / Biso mean: 34.0311 Å2 / Biso min: 4.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 231 48 20 299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021312
X-RAY DIFFRACTIONr_angle_refined_deg1.6083478
X-RAY DIFFRACTIONr_chiral_restr0.0590.245
X-RAY DIFFRACTIONr_gen_planes_refined0.0210.02169
X-RAY DIFFRACTIONr_scbond_it2.8643312
X-RAY DIFFRACTIONr_scangle_it4.4284.5478
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 5 -
Rwork0.381 114 -
all-119 -
obs--92.97 %

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