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- PDB-7klp: Crystal structure of a three-tetrad, parallel, K+ stabilized huma... -

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Basic information

Entry
Database: PDB / ID: 7klp
TitleCrystal structure of a three-tetrad, parallel, K+ stabilized human telomeric G-quadruplex
Componentstelomeric DNA
KeywordsDNA / three-quartets / Parallel / G-quadruplex / Propeller Loops / human telomeric DNA
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsYatsunyk, L.A. / Li, K.S. / Chen, E.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA208676-01A1 United States
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: Water spines and networks in G-quadruplex structures.
Authors: Li, K. / Yatsunyk, L. / Neidle, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of a three-tetrad, parallel, K + -stabilized human telomeric G-quadruplex at 1.35 angstrom resolution.
Authors: Chen, E.V. / Nicoludis, J.M. / Powell, B.M. / Li, K.S. / Yatsunyk, L.A.
History
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: telomeric DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4617
Polymers6,9831
Non-polymers4786
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, demonstrates that the DNA adopts a monomolecular structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.686, 56.686, 42.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-104-

K

31A-105-

K

41A-202-

HOH

51A-263-

HOH

61A-310-

HOH

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Components

#1: DNA chain telomeric DNA


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.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.1 % / Description: small square bipyramides
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 50 mM Li Cac pH 7.2, 200 mM KCl, 500 mM (NH4)2SO4, 23% PEG400

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.34→49.17 Å / Num. obs: 32545 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 19.57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Rrim(I) all: 0.051 / Net I/σ(I): 17.3
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 8.2 % / Rmerge(I) obs: 6.026 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 809 / CC1/2: 0.32 / Rpim(I) all: 2.187 / Rrim(I) all: 6.423 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
PHENIX1.18.2_3874phasing
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FXM

4fxm


Resolution: 1.35→42.31 Å / SU ML: 0.1627 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.4905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1761 1454 10.03 %
Rwork0.142 13048 -
obs0.1455 14502 84.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 1.35→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 465 24 111 600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127663
X-RAY DIFFRACTIONf_angle_d1.41381020
X-RAY DIFFRACTIONf_chiral_restr0.076106
X-RAY DIFFRACTIONf_plane_restr0.010927
X-RAY DIFFRACTIONf_dihedral_angle_d30.8997284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.40.34131030.3648838X-RAY DIFFRACTION56.01
1.4-1.450.38761040.2962990X-RAY DIFFRACTION63.64
1.45-1.520.33771110.27511063X-RAY DIFFRACTION69.67
1.52-1.60.24171420.21461223X-RAY DIFFRACTION80.29
1.6-1.70.17241570.14381358X-RAY DIFFRACTION88.24
1.7-1.830.18111550.15141437X-RAY DIFFRACTION93.37
1.83-2.020.211660.16441488X-RAY DIFFRACTION96.22
2.02-2.310.22841650.1771517X-RAY DIFFRACTION98.71
2.31-2.910.18581730.15531544X-RAY DIFFRACTION99.71
2.91-42.310.13671780.1051590X-RAY DIFFRACTION99.66

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