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- PDB-6ip3: Structure of human telomeric DNA at 1.4 Angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 6ip3
TitleStructure of human telomeric DNA at 1.4 Angstroms resolution
ComponentsDNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
KeywordsDNA / Human telomere / parallel G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSaikrishnan, K. / Nuthanakanti, A. / Srivatsan, S.G. / Ahmad, I.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome TrustIA/S/16/1/502360 India
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe.
Authors: Nuthanakanti, A. / Ahmed, I. / Khatik, S.Y. / Saikrishnan, K. / Srivatsan, S.G.
History
DepositionNov 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Nov 22, 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
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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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Assembly

Deposited unit
A: DNA (5'-D(*AP*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)7,1014
Polymers6,9831
Non-polymers1173
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-0 kcal/mol
Surface area4570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.839, 56.839, 42.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-103-

K

21A-209-

HOH

31A-252-

HOH

41A-268-

HOH

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Components

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


Mass: 6983.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05M sodium cacodylate (pH = 7.2), 0.4M ammonium sulfate, 0.05M KCl, 0.01M CaCl2, 15% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 15493 / % possible obs: 100 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 16.4
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 777 / Rsym value: 0.88

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KF1

1kf1


Resolution: 1.4→28.42 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1727 797 5.15 %
Rwork0.1512 --
obs0.1523 15469 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→28.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 465 3 79 547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01645
X-RAY DIFFRACTIONf_angle_d0.991003
X-RAY DIFFRACTIONf_dihedral_angle_d30.386268
X-RAY DIFFRACTIONf_chiral_restr0.063106
X-RAY DIFFRACTIONf_plane_restr0.00927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.48780.22561320.17442425X-RAY DIFFRACTION100
1.4878-1.60270.17771290.1422413X-RAY DIFFRACTION100
1.6027-1.7640.14771110.11062462X-RAY DIFFRACTION100
1.764-2.01920.17151380.14212439X-RAY DIFFRACTION100
2.0192-2.54370.18441230.1642465X-RAY DIFFRACTION100
2.5437-28.42550.16841640.15592468X-RAY DIFFRACTION100

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