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- PDB-4da3: Crystal structure of an intramolecular human telomeric DNA G-quad... -

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Basic information

Entry
Database: PDB / ID: 4da3
TitleCrystal structure of an intramolecular human telomeric DNA G-quadruplex 21-mer bound by the naphthalene diimide compound MM41.
ComponentsDNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
KeywordsDNA / intramolecular / ligand-complex / G-quadruplex / telomere
Function / homologyChem-0DX / : / DNA / DNA (> 10)
Function and homology information
Biological speciesSynthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCollie, G.W. / Neidle, S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structure-based design and evaluation of naphthalene diimide g-quadruplex ligands as telomere targeting agents in pancreatic cancer cells.
Authors: Micco, M. / Collie, G.W. / Dale, A.G. / Ohnmacht, S.A. / Pazitna, I. / Gunaratnam, M. / Reszka, A.P. / Neidle, S.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Database references
Revision 1.3Sep 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 / 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 / _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_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_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6195
Polymers6,6701
Non-polymers9484
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.310, 51.310, 51.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-103-

K

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 6670.290 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA synthesized by standard phosphoramidite chemistry.
Source: (synth.) Synthetic DNA (others)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-0DX / 4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}-2,7-bis[3-(morpholin-4-yl)propyl]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone


Mass: 831.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H66N10O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.96 Å3/Da / Density % sol: 58.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG400, 150 mM sodium chloride and 50 mM sodium cacodylate (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.27→25.97 Å / Num. all: 3843 / Num. obs: 3843 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 66.213 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.9
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique all: 278 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SC8

3sc8


Resolution: 2.4→14.81 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.523 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28202 151 4.6 %RANDOM
Rwork0.24221 ---
obs0.24424 3098 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.532 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→14.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 444 63 25 532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.012567
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.505869
X-RAY DIFFRACTIONr_chiral_restr0.070.263
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02261
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.571 9 -
Rwork0.457 196 -
obs--99.03 %

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