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- PDB-3r6r: Structure of the complex of an intramolecular human telomeric DNA... -

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Basic information

Entry
Database: PDB / ID: 3r6r
TitleStructure of the complex of an intramolecular human telomeric DNA with Berberine formed in K+ solution
ComponentsDNA (22-mer)
KeywordsDNA/ANTIBIOTIC / DNA-DRUG COMPLEX / G-QUADRUPLEX / HUMAN TELOMERIC DNA / DNA / DNA-ANTIBIOTIC complex
Function / homologyBERBERINE / : / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1.
Authors: Bazzicalupi, C. / Ferraroni, M. / Bilia, A.R. / Scheggi, F. / Gratteri, P.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: DNA (22-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4077
Polymers6,9831
Non-polymers1,4246
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.620, 65.620, 41.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-27-

BER

21A-28-

BER

31A-30-

HOH

41A-42-

HOH

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Components

#1: DNA chain DNA (22-mer)


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: telomeric DNA
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-BER / BERBERINE / Berberine


Mass: 336.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H18NO4 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.72 Å3/Da / Density % sol: 66.94 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: Ammonium sulphate, Lithium sulphate, potassium chloride, pH 6.5, vapor diffusion, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2010
RadiationMonochromator: Double crystal Si(111), horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→56.828 Å / Num. all: 4674 / Num. obs: 4674 / % possible obs: 100 % / Redundancy: 22.2 % / Rsym value: 0.088 / Net I/σ(I): 24.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.4222.30.6811.1150146730.681100
2.42-2.5722.40.4531.7142596370.453100
2.57-2.7522.40.272.8135576060.27100
2.75-2.9722.40.2033.8125555610.203100
2.97-3.2522.30.0717.8115535180.071100
3.25-3.6422.30.0457.7104744690.045100
3.64-4.222.20.0718.791424110.071100
4.2-5.1422.10.089679053580.089100
5.14-7.2721.70.0678.959782760.067100
7.27-41.8120.20.0311833371650.03199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å41.81 Å
Translation3.5 Å41.81 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry code 3CDM

3cdm


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2498 / WRfactor Rwork: 0.2106 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8045 / SU ML: 0.162 / SU R Cruickshank DPI: 0.3252 / SU Rfree: 0.2389 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 188 4.6 %RANDOM
Rwork0.2155 ---
obs0.2172 4128 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.16 Å2 / Biso mean: 26.147 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 465 102 29 596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021640
X-RAY DIFFRACTIONr_angle_refined_deg2.4513984
X-RAY DIFFRACTIONr_chiral_restr0.0580.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02344
X-RAY DIFFRACTIONr_mcbond_it0.1991.512
X-RAY DIFFRACTIONr_mcangle_it0.377216
X-RAY DIFFRACTIONr_scbond_it1.1333628
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 16 -
Rwork0.422 294 -
all-310 -
obs--100 %

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