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- PDB-6ip7: Structure of human telomeric DNA with 5-Selenophene-modified deox... -

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Basic information

Entry
Database: PDB / ID: 6ip7
TitleStructure of human telomeric DNA with 5-Selenophene-modified deoxyuridine at residue 11
ComponentsDNA (22-MER)
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: 1.55 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 2, 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 / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_symmetry / _struct_conn_type.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)7,2004
Polymers7,0821
Non-polymers1173
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-0 kcal/mol
Surface area4530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.483, 56.483, 42.415
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-221-

HOH

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Components

#1: DNA chain DNA (22-MER)


Mass: 7082.490 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: isolated from a natural source / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.05M potassium cacodylate (pH7.2), 0.625M ammonium acetate, 0.2M KCl, 15% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 22608 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 23.6
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.898 / Num. unique obs: 563 / Rsym value: 0.898

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Processing

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

1kf1


Resolution: 1.55→48.916 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER F_MINUS AND F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2129 1115 5.09 %
Rwork0.1893 --
obs0.1907 21923 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→48.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 469 3 50 522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012529
X-RAY DIFFRACTIONf_angle_d1.424819
X-RAY DIFFRACTIONf_dihedral_angle_d29.814212
X-RAY DIFFRACTIONf_chiral_restr0.07386
X-RAY DIFFRACTIONf_plane_restr0.01223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.62060.26841420.26072622X-RAY DIFFRACTION99
1.6206-1.7060.20761200.20072579X-RAY DIFFRACTION99
1.706-1.81290.3095980.19672632X-RAY DIFFRACTION100
1.8129-1.95290.2711500.23442597X-RAY DIFFRACTION100
1.9529-2.14940.26051340.23132602X-RAY DIFFRACTION100
2.1494-2.46050.18271360.20432620X-RAY DIFFRACTION100
2.4605-3.09990.22111560.20932589X-RAY DIFFRACTION100
3.0999-48.94010.19461790.15592567X-RAY DIFFRACTION99

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