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- PDB-4p1d: Structure of the complex of a bimolecular human telomeric DNA wit... -

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Basic information

Entry
Database: PDB / ID: 4p1d
TitleStructure of the complex of a bimolecular human telomeric DNA with Coptisine
Componentstelomeric DNA
KeywordsDNA / DRUG-DNA COMPLEX / G-QUADRUPLEX
Function / homology: / Chem-KPT / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsFerraroni, M. / Bazzicalupi, C. / Gratteri, P.
CitationJournal: to be published
Title: Crystal Structure of the complex of a bimolecular human telomeric DNA with Coptisine
Authors: Ferraroni, M. / Bazzicalupi, C. / Gratteri, P. / Bilia, A.R. / Sissi, C.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / pdbx_database_status ...citation / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_database_status.pdb_format_compatible ..._citation.journal_id_CSD / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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_radiation_wavelength / pdbx_initial_refinement_model / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,9455
Polymers7,5472
Non-polymers3993
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-6 kcal/mol
Surface area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.567, 41.567, 66.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asymmetric unit

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Components

#1: DNA chain 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-KPT / 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium / Coptisine


Mass: 320.319 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14NO4 / Comment: alkaloid*YM
#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: 1.89 Å3/Da / Density % sol: 35.03 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sodium Fluoride, Potassium Fluoride, Cacodylate, MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2012
RadiationMonochromator: Double crystal Si(111), horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.002 Å / Relative weight: 1
ReflectionResolution: 1.55→35.2 Å / Num. obs: 8899 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 18.7 % / Biso Wilson estimate: 28.609 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.117 / Χ2: 0.971 / Net I/σ(I): 15.22 / Num. measured all: 166071
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
1.55-1.6413.90.9960.742.0818967139713680.76797.9
1.64-1.7610.3224.9527666131613160.33100
1.76-1.90.9960.5656.3224931125412540.58100
1.9-2.080.9940.39510.5223763113711370.405100
2.08-2.320.9970.25316.6120578104410440.26100
2.32-2.680.9980.12324.29186649349340.127100
2.68-3.280.9950.08731.92145688058040.0999.9
3.28-4.610.9980.0838.53109226486470.08399.8
4.610.9980.07339.4560123963950.07699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE2.1.4data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K8P

1k8p


Resolution: 1.55→35.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2813 / WRfactor Rwork: 0.2407 / FOM work R set: 0.7267 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1094 / SU Rfree: 0.1048 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 444 5 %RANDOM
Rwork0.2316 8436 --
obs0.2331 8880 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.24 Å2 / Biso mean: 28.9632 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 1.55→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 502 26 28 556
Biso mean--20.26 36.67 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.014593
X-RAY DIFFRACTIONr_angle_refined_deg2.4721.695916
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A''3)0.1290.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02292
X-RAY DIFFRACTIONSIDE-CHAIN BOND REFINED ATOMS (A''2)2.5822.833591
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.597 30 -
Rwork0.494 579 -
all-609 -
obs--96.36 %

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