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- PDB-5dwx: Structural Insights into the Quadruplex-Duplex 3' Interface forme... -

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Basic information

Entry
Database: PDB / ID: 5dwx
TitleStructural Insights into the Quadruplex-Duplex 3' Interface formed from a Telomeric Repeat - TLOOP
Components
  • DNA (24-MER)
  • DNA complementary strand
KeywordsDNA / Telomere / Quadruplex / Junction / Duplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsParkinson, G.N. / Russo Krauss, I.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target.
Authors: Russo Krauss, I. / Ramaswamy, S. / Neidle, S. / Haider, S. / Parkinson, G.N.
History
DepositionSep 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Jan 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 / pdbx_struct_conn_angle / struct_conn
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.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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (24-MER)
B: DNA complementary strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1375
Polymers10,0192
Non-polymers1173
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint2 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.830, 59.830, 72.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-103-

K

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Components

#1: DNA chain DNA (24-MER)


Mass: 7608.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA complementary strand


Mass: 2410.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 2 M lithium sulphate, 50 mM Tris/HCl pH 8.8 2 mM CuCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.71→42.31 Å / Num. obs: 3820 / % possible obs: 98.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 12.3
Reflection shellResolution: 2.71→2.78 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.93 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF1

1kf1


Resolution: 2.71→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.864 / SU B: 11.596 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.442 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32705 170 4.5 %RANDOM
Rwork0.28462 ---
obs0.28669 3632 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-0 Å2
2--0.14 Å2-0 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 2.71→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 502 3 0 505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.011564
X-RAY DIFFRACTIONr_bond_other_d0.0010.02272
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.14872
X-RAY DIFFRACTIONr_angle_other_deg2.3383644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2220.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.02300
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02116
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.6685.291564
X-RAY DIFFRACTIONr_scbond_other6.6625.293565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.8697.9873
X-RAY DIFFRACTIONr_long_range_B_refined15.3947.5452414
X-RAY DIFFRACTIONr_long_range_B_other15.39247.5712413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.711→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 10 -
Rwork0.363 249 -
obs--96.64 %

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