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- PDB-6pnk: Crystal structure of the G-quadruplex formed by (GGGTT)3GGG in co... -

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Basic information

Entry
Database: PDB / ID: 6pnk
TitleCrystal structure of the G-quadruplex formed by (GGGTT)3GGG in complex with N-methylmesoporphryin IX
ComponentsDNA (5'-D(P*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*G)-3')
KeywordsDNA / parallel G-quadruplex / end-stacking / TT propeller loops
Function / homologyFORMIC ACID / : / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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
DepositionJul 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / 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 / _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_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_symmetry
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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*G)-3')
B: DNA (5'-D(P*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,92612
Polymers11,4612
Non-polymers1,46510
Water00
1
A: DNA (5'-D(P*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*G)-3')
hetero molecules


  • defined by author
  • 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
  • 6.43 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)6,4295
Polymers5,7311
Non-polymers6984
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (5'-D(P*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*GP*TP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4987
Polymers5,7311
Non-polymers7676
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.930, 60.930, 194.342
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-103-

K

21B-102-

K

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Components

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


Mass: 5730.669 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.: 6 / Source method: obtained synthetically / 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: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY

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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: 3.03 Å3/Da / Density % sol: 59.39 % / Description: Hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.85 M sodium formate, 17.5% PEG 20000, 0.05 M Bis-Tris 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: 2.388→64.78 Å / Num. obs: 5748 / % possible obs: 97.5 % / Redundancy: 19 % / Biso Wilson estimate: 90.97 Å2 / CC1/2: 0.369 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.4
Reflection shellResolution: 2.388→2.473 Å / Redundancy: 19 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 492 / CC1/2: 0.369 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P45

6p45


Resolution: 2.39→64.78 Å / SU ML: 0.2982 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.4204
RfactorNum. reflection% reflectionSelection details
Rfree0.249 567 9.98 %Random selection
Rwork0.2352 ---
obs0.2364 5748 97.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 115.44 Å2
Refinement stepCycle: LAST / Resolution: 2.39→64.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 707 80 0 787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086912
X-RAY DIFFRACTIONf_angle_d1.76061406
X-RAY DIFFRACTIONf_chiral_restr0.0421135
X-RAY DIFFRACTIONf_plane_restr0.007242
X-RAY DIFFRACTIONf_dihedral_angle_d36.1424345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.630.36971330.3351204X-RAY DIFFRACTION93.5
2.63-3.010.32031400.29071272X-RAY DIFFRACTION99.3
3.01-3.790.25461410.25451270X-RAY DIFFRACTION96.98
3.79-64.780.23421530.21911371X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: -15.9855156741 Å / Origin y: 8.42790186784 Å / Origin z: -48.7943706657 Å
111213212223313233
T0.725145392764 Å20.0102165038131 Å20.0117954157429 Å2-0.724605098783 Å20.0871415756062 Å2--0.864727199319 Å2
L3.18484288651 °21.17728661171 °25.31910371751 °2-2.05842395255 °22.95265405947 °2--7.36732476833 °2
S0.129713427349 Å °-0.172400951046 Å °-0.030643519396 Å °0.22607509106 Å °-0.335528147407 Å °0.379147484125 Å °0.453319152636 Å °-0.521429315118 Å °0.144472145701 Å °
Refinement TLS groupSelection details: all

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