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- PDB-6h5r: Structure of the complex of a human telomeric DNA with bis(1-buty... -

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Basic information

Entry
Database: PDB / ID: 6h5r
TitleStructure of the complex of a human telomeric DNA with bis(1-butyl-3-methyl-imidazole-2-ylidene) gold(I)
ComponentsHuman Telomeric DNA
KeywordsDNA / DRUG-DNA COMPLEX / G quadruplex
Function / homologybis(1-butyl-3-methyl-imidazol-3-ium-2-yl)gold / : / STRONTIUM ION / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBazzicalupi, C. / Gratteri, P. / Papi, F.
CitationJournal: Dalton Trans / Year: 2018
Title: Interaction of a gold(i) dicarbene anticancer drug with human telomeric DNA G-quadruplex: solution and computationally aided X-ray diffraction analysis.
Authors: Guarra, F. / Marzo, T. / Ferraroni, M. / Papi, F. / Bazzicalupi, C. / Gratteri, P. / Pescitelli, G. / Messori, L. / Biver, T. / Gabbiani, C.
History
DepositionJul 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Human Telomeric DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6518
Polymers7,5921
Non-polymers2,0597
Water70339
1
A: Human Telomeric DNA
hetero molecules

A: Human Telomeric DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,30216
Polymers15,1842
Non-polymers4,11914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2610 Å2
ΔGint-131 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.600, 71.370, 27.050
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-216-

HOH

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Components

#1: DNA chain Human Telomeric DNA


Mass: 7591.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Chemical
ChemComp-FTQ / bis(1-butyl-3-methyl-imidazol-3-ium-2-yl)gold


Mass: 473.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H28AuN4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5 / Details: isopropanol, KCacodylate, Li2SO4, MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2→35.69 Å / Num. obs: 8883 / % possible obs: 97.6 % / Redundancy: 5.4 % / CC1/2: 0.99 / Rrim(I) all: 0.12 / Rsym value: 0.11 / Net I/σ(I): 6.04
Reflection shellResolution: 1.69→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 2.65 / Num. unique obs: 1307 / CC1/2: 0.22 / Rrim(I) all: 3 / Rsym value: 0.6 / % possible all: 90.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R6R

3r6r


Resolution: 2→35.69 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2754 / WRfactor Rwork: 0.2495 / FOM work R set: 0.788 / SU B: 5.018 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2898 / SU Rfree: 0.2036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.29 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 517 11 %RANDOM
Rwork0.2284 ---
obs0.2309 4178 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 220.49 Å2 / Biso mean: 44.038 Å2 / Biso min: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.12 Å2
2--4.1 Å20 Å2
3----3.58 Å2
Refinement stepCycle: final / Resolution: 2→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 504 81 39 624
Biso mean--46.47 59.02 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.012649
X-RAY DIFFRACTIONr_bond_other_d0.0020.02379
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.353987
X-RAY DIFFRACTIONr_angle_other_deg2.6453886
X-RAY DIFFRACTIONr_chiral_restr0.3170.279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02128
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 41 -
Rwork0.316 296 -
all-337 -
obs--98.83 %

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