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- PDB-5cdb: Structure of the complex of a bimolecular human telomeric DNA wit... -

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Basic information

Entry
Database: PDB / ID: 5cdb
TitleStructure of the complex of a bimolecular human telomeric DNA with a 13-diphenylalkyl Berberine derivative
Componentshuman telomeric DNA
KeywordsDNA / DRUG-DNA COMPLEX / G-QUADRUPLEX
Function / homology13-diphenylalkyl Berberine / : / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P. / Papi, F.
CitationJournal: Chem Asian J / Year: 2016
Title: Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes.
Authors: Ferraroni, M. / Bazzicalupi, C. / Papi, F. / Fiorillo, G. / Guaman-Ortiz, L.M. / Nocentini, A. / Scovassi, A.I. / Lombardi, P. / Gratteri, P.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human telomeric DNA
B: human telomeric DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1705
Polymers7,5472
Non-polymers6233
Water50428
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-8 kcal/mol
Surface area4560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.132, 41.132, 71.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: DNA chain human telomeric DNA


Mass: 3773.462 Da / Num. of mol.: 2 / 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-50B / 13-diphenylalkyl Berberine


Mass: 544.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C36H34NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulphate, lithium sulphate, sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.62 Å / Num. obs: 7183 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 25.5 % / Biso Wilson estimate: 47.638 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Χ2: 1.128 / Net I/σ(I): 20.83 / Num. measured all: 183179
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.811.90.9822.0120.8412699113810612.10393.2
1.8-1.920.7872.4441.2220866107310732.51100
1.92-2.080.8961.5922.6731103100510051.619100
2.08-2.270.9780.7895.57278579279270.803100
2.27-2.540.9970.32813.1268828468460.333100
2.54-2.9310.12128.35225907627620.123100
2.93-3.5810.04156.92187056516510.042100
3.58-5.0410.04179.71145345235230.041100
5.040.9990.03884.0779433353350.039100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.45 Å29.08 Å
Translation4.45 Å29.08 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P1D

4p1d


Resolution: 1.7→35.62 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2935 / WRfactor Rwork: 0.2343 / FOM work R set: 0.6624 / SU B: 4.681 / SU ML: 0.131 / SU R Cruickshank DPI: 0.1397 / SU Rfree: 0.1409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 355 5 %RANDOM
Rwork0.2311 ---
obs0.2335 7120 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.8 Å2 / Biso mean: 45.885 Å2 / Biso min: 29.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 1.7→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 482 43 28 553
Biso mean--52.72 60.87 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.014589
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.679905
X-RAY DIFFRACTIONr_chiral_restr0.1050.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02286
X-RAY DIFFRACTIONr_scbond_it3.2914.863587

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