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- PDB-7zur: Four carbons pendant pyridine derivative of the natural alkaloid ... -

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Basic information

Entry
Database: PDB / ID: 7zur
TitleFour carbons pendant pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder
ComponentsDNA TAGGGTTAGGGT
KeywordsDNA / DRUG-DNA COMPLEX / telomeric G-quadruplex
Function / homology: / Chem-K0F / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBazzicalupi, C. / Ferraroni, M. / Gratteri, P. / Papi, F.
Funding support Italy, 2items
OrganizationGrant numberCountry
Other privateISP B/2021/0168 Italy
Other privateECR 23942_2019 Italy
CitationJournal: Int J Mol Sci / Year: 2022
Title: Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis.
Authors: Bazzicalupi, C. / Bonardi, A. / Biver, T. / Ferraroni, M. / Papi, F. / Savastano, M. / Lombardi, P. / Gratteri, P.
History
DepositionMay 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA TAGGGTTAGGGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3214
Polymers3,7731
Non-polymers5483
Water362
1
A: DNA TAGGGTTAGGGT
hetero molecules

A: DNA TAGGGTTAGGGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6428
Polymers7,5472
Non-polymers1,0956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)42.100, 42.100, 34.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-103-

K0F

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Components

#1: DNA chain DNA TAGGGTTAGGGT


Mass: 3773.462 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-K0F / 16,17-dimethoxy-21-(4-pyridin-4-ylbutyl)-5,7-dioxa-13$l^{4}-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2(10),3,8,13,15,17,19-octaene / Berberine


Mass: 469.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H29N2O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.93 Å3/Da / Density % sol: 0.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Kcacodylate, Li2SO4, PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97264 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97264 Å / Relative weight: 1
ReflectionResolution: 1.49→29.77 Å / Num. obs: 5252 / % possible obs: 98.2 % / Redundancy: 10.697 % / Biso Wilson estimate: 51.743 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.065 / Χ2: 1.077 / Net I/σ(I): 9.2 / Num. measured all: 56180 / Scaling rejects: 29
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
1.49-1.586.27710.453193.9
1.58-1.6910.37980.9351100
1.69-1.82127440.999199.9
1.82-212.16820.9881100
2-2.2312.36270.9941100
2.23-2.5812.15630.9961100
2.58-3.1511.34840.998199.8
3.15-4.4310.73880.997199.5
4.43-10.6979.42460.998199.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0151refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CDB

5cdb


Resolution: 1.6→29.77 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.961 / SU B: 10.715 / SU ML: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3099 418 9.6 %RANDOM
Rwork0.2816 ---
obs0.2845 3925 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.83 Å2 / Biso mean: 78.865 Å2 / Biso min: 41.65 Å2
Baniso -1Baniso -2Baniso -3
1-3.4 Å2-0 Å2-0 Å2
2--3.4 Å2-0 Å2
3----6.79 Å2
Refinement stepCycle: final / Resolution: 1.6→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 250 66 2 318
Biso mean--56.05 70.24 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.011336
X-RAY DIFFRACTIONr_bond_other_d0.0030.018170
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.177517
X-RAY DIFFRACTIONr_angle_other_deg1.8193400
X-RAY DIFFRACTIONr_chiral_restr0.0870.238
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02332
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0269
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree1 32 -
Rwork0.966 278 -
obs--99.04 %

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