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- PDB-6p45: Crystal structure of the G-quadruplex formed by (TGGGT)4 in compl... -

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Basic information

Entry
Database: PDB / ID: 6p45
TitleCrystal structure of the G-quadruplex formed by (TGGGT)4 in complex with N-methylmesoporphryin IX
ComponentsDNA (5'-D(P*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
KeywordsDNA / parallel G-quadruplex / N-methymesoporphyrin IX / end-stacking / TT propeller loops
Function / homology: / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.339 Å
AuthorsYatsunyk, L.A. / Lin, L.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)1R15CA208676-01A1 United States
CitationJournal: Plos One / Year: 2020
Title: Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX.
Authors: Lin, L.Y. / McCarthy, S. / Powell, B.M. / Manurung, Y. / Xiang, I.M. / Dean, W.L. / Chaires, B. / Yatsunyk, L.A.
History
DepositionMay 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(P*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
B: DNA (5'-D(P*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0359
Polymers12,6782
Non-polymers1,3577
Water724
1
A: DNA (5'-D(P*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
hetero molecules


  • defined by author&software
  • Evidence: equilibrium centrifugation, determined purity and oligomerization state, isothermal titration calorimetry, determined binding constants and thermodynamics of binding, native gel ...Evidence: equilibrium centrifugation, determined purity and oligomerization state, isothermal titration calorimetry, determined binding constants and thermodynamics of binding, native gel electrophoresis, determined purity and homogeneity of the samples, mass spectrometry, determined binding stoichiometry and binding constants
  • 7.04 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)7,0375
Polymers6,3391
Non-polymers6984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA (5'-D(P*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9984
Polymers6,3391
Non-polymers6593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.280, 59.280, 63.332
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: DNA chain DNA (5'-D(P*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*T)-3')


Mass: 6339.056 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: K
#3: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H40N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.53 Å3/Da / Density % sol: 51.46 % / Description: Hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 3.5 M lithium chloride, 0.03 M magnesium chloride, 0.05 M HEPES sodium pH 7.0

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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: Mar 10, 2018
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.339→51.34 Å / Num. obs: 5377 / % possible obs: 98.82 % / Redundancy: 9.5 % / Biso Wilson estimate: 71.28 Å2 / CC1/2: 1 / R split: 0.039 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.027 / Rrim(I) all: 0.083 / Net I/σ(I): 14.9
Reflection shellResolution: 2.339→2.423 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 498 / CC1/2: 0.367 / % possible all: 92.39

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FXM

4fxm


Resolution: 2.339→51.338 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.08
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 535 9.99 %Random selection
Rwork0.2001 ---
obs-5355 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.339→51.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 783 75 4 862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01957
X-RAY DIFFRACTIONf_angle_d1.7441479
X-RAY DIFFRACTIONf_dihedral_angle_d36.511384
X-RAY DIFFRACTIONf_chiral_restr0.095149
X-RAY DIFFRACTIONf_plane_restr0.00842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3392-2.57460.2951290.26891175X-RAY DIFFRACTION97
2.5746-2.94710.31881410.281199X-RAY DIFFRACTION100
2.9471-3.71290.21031290.19791213X-RAY DIFFRACTION99
3.7129-51.35030.20811360.18341233X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -18.7873 Å / Origin y: 1.528 Å / Origin z: 0.6068 Å
111213212223313233
T0.4032 Å20.023 Å20.0241 Å2-0.4114 Å20.0935 Å2--0.6725 Å2
L10.8955 °2-2.4376 °2-0.7208 °2-8.063 °22.8575 °2--11.8098 °2
S-0.4673 Å °0.0675 Å °-0.2748 Å °0.5059 Å °0.3469 Å °0.5035 Å °0.6098 Å °-0.2433 Å °0.0847 Å °
Refinement TLS groupSelection details: all

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